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Corelyzer User`s Manual

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1. TTA Siding ai tracks es oorr ere p ester tesa ero E te P yer eoe EON EOE ei 64 7 2 Graph Plots Sx erede et eed a VE t esce ul te UI EUR babe 65 7 2 1 Graph plot properties scaling ssessse Hee 65 7 2 2 Graph plot properties colors sssssss mee 65 AD VITSE ON RR NE 67 8 1 Creating new annotations desses eorn eio ere te re P eR et duce vede em d ts 67 8 2 Reviewing and editing existing annotations ssesseseeee He 68 8 3 Measuring M dE eoe DINER o ROI WR 70 9 Save and Load Sessions cria e RE E E EE ENE IEE NE oE 73 10 Corelyzer server and plugin clients sees emere 74 10 1 Server ME PEE 74 10 2 Runnmnp the servens coe Sea ceeds etr poe ener et exor eens te EEE es SEIS 75 10 3 Running the administration client ssssesssssese eee ene 75 10 4 Administrator commands ssssssssssesee ee emen Hehe hee nre 75 10 5 Admin commands reference table sssssssss e 77 10 6 Cheni pl gim n Corelyzer eoe IRI e TI 10 7 Ex mple dataset file eec eot ren mettere aede ee Prose e xe rere deep nU d 80 10 8 Handy Scripts so RES OE e RENE da eee e E et 81 10 9 SOME notes ocior te br eit E dean tweneee e Meca oct Po dee cioe tieu es Ede etes ec cot dest 81 TI Eme tune with Correlator J A reete ertet Wieser hl Behe eles 82 11 1 Before start Download Corrlator and Corelyzer sess 82 11 2 Interaction Tow tis
2. Annotation Figure 8 7 Enable measure mode s e she cx Measure mode Help Measure History Measure 3m 28 6cm H4 PointO 328 59 6 26 Pointi 331 93 10 38 Distance 5 31 cm Figure 8 8 Show measuring history Measure mode elp Measure History i Measure 3m 28 6cm Measure 3m 31 8cm Measure 3m 29 7cm Measure 3m 29 8cm 71 Annotation Figure 8 9 Measure on images A screen capture video of these actions can be found in this link online size 5 7MB http www evl uic edu cavern corewall documents movies 8 3 Measure move 72 Chapter 9 Save and Load Sessions You can save your current working session by selecting Save Session As under File menu This function will save all the information that you loaded into the scene into a XML based CML file CML file schema description can be found in here http instaar colorado edu 7Ejenkinsc dbseabed corewall CmlXml Syntax 1 pdf This file doesn t save all the images and dataset files with it it keeps track of where all the related files are located You can later load everything back by selecting Open a Session File under the same File menu The cml file is small and if the resource you loaded into the scene are all downloaded from the Internet within Corelyzer these resources URL will be kept and by passing just the cml file around other people can load back the same sessio
3. But users should be aware that the FMS images are not cropped to the exact range and there are white space form borders around the image so the estimatation may not be accurate If you want further finer adjustment could be adjusted in the images properties dialog A screen capture video of these actions can be found in this link online size 6MB in 1920x1200 resolution http www evl uic edu cavern corewall documents movies LoadFromLoggingDB mov 45 Chapter 6 Load and Plot Numerical Log Data 6 1 Native Corelyzer XML Format Dataset Files Corelyzer loads data using the Corelyzer data XML schema see appendix A Corelyzer XML format datset file can contain multiple fields in a single file Data files can be loaded at anytime during the execution of the program To do so you will need to choose the menu item under File gt Open Dataset Files and a file selection dialog will appear Corelyzer data files are in XML and properly have a xml extension appended to them Once a data file is selected the Corelyzer application will process the data and then update the Dataset and Fields list boxes click on the Local label in My Core Repository to show the lists If you load up multiple data files you can click on a dataset to view what fields were retrieved from the data file A screen capture video of these actions can be found in this link online size 868KB http www evl uic edu cavern corewall documents movies 6 1
4. DPI and start depth and depth increment Click on Apply button will update and fill specified parameters into the table above Click OK button when you are satisfied with the table content Corelyzer will start loading selected images with specified parameters Figure 5 2 Load Images dialog AOD ooo m a Image Files and Properties Saheer image Files Fin aree enuon bergh DFN DALY Depth im GLAD4 HSTO3 A M 2 pq Vertical 1 5 n 1 5 GLADA HSTG3 DA 2M l pg Vertical LS n 9 3 Reiet C Batch input Orientation Length imeterk DR Stan Depth imeterk Depth increment retest a tor Hele Came er 30 Load Images Once completed the visualization window will display our imagery and the Section listbox in the main iCores control window will update with the image filenames loaded on the Track Notice in the image below that our image has a ruler in it and that the ruler in the image closely matches the markers indicating depth at the bottom of the visualization window Figure 5 3 Visualization canvas with loaded core section images A screen capture video of these actions can be found in this link online size 3 5MB http www evl uic edu cavern corewall documents movies 5 1 LoadLocalImages mov 5 2 Load Images from online services Corelyzer was built in a simple interface to access online core image services like the IODP Janus database and IODP LIMS service to retr
5. To load FMS images from the IODP USIO logging database select the IODP meun item from the File menu and then select Show IODP lists Then clicking on the Logging DB tab in the popup window as shown in the following figure 43 Load Images Figure 5 15 Logging DB tab in IODP tables window Site G4z2E Tool FMg Site Hale 306 B42E FMS 306 B42E FMS 306 B42E FMS 306 642E FMS 306 B42E FMS 306 b42E FMS 306 B42E FMS 306 B42E FMS 306 B4ZE FMS 306 B42E FMS 306 B42E FMS 306 B42E FMS 306 B42E FMS 306 b42E FMS 306 642E FMS 306 B42E FMS 306 642E FMS 306 amp 42E FMS 306 B42E FMS 306 B42E FMS 306 amp 42E FMS 306 B42E FMS Data files Section list Affine table Service provid http brg ldeo columbia edu services Measurement Splice table Filename borehole electri Fass 1 Dynami borehole electri Pass 1 Oynam borehole lectri Pass 1 Dynam borehole electri Fass 2 Dynami borehole electri Pass 1 Static 3 borehole electri Fass 1 Static 3 borehole electri Pass 1 Static 4 borehole electri Pass 2 Static 3 borehole electri Pass 1 Dynam borehole electri Pass 1 Dynam borehole electri Fass 1 Dynami borehole electri Pass 1 Oynam borehole electri Pass 1 Dynam borehole electri Pass 1 Dynam borehole electri Pass 1 Oynam b rehole electri Pass 1 Dyrnar borehole electri Pass 1 Dynami borehole electri Pass 1 Dynam borehole electri Fass 1
6. 0278 Ora 19 336 0422 2 7477 2 5019 0 3589 0 0278 0 0747 20 336 1946 2 2477 2 5013 0 3589 Q 0z 7 amp 0 0747 21 334 3470 2 2477 2 5013 0 3589 0 0278 0 0747 zi 336 4994 ATE 2 5019 0 3589 0278 0 0747 2331366518 3 2477 2 5013 0 3583 O02 78 Ora 24 336 8042 2 7477 2 5019 0 3589 0 0278 0 0747 25 336 9566 IT 2 5013 0 3583 Q 0z 78 0 0747 26 337 1090 2 2477 2 5013 0 3589 0 0278 0 0747 if 337 2014 afar 2 5013 0 3589 0278 0 0747 28 3374138 2 5477 2 5013 0 3549 O 0278 Ora i 29 137 5662 2 7477 2 5018 0 3589 02 78 0 0747 gini ui C Cad COO Bk Ne Next you need to specify the lines showing the labels for fields and units If the data file does not have the unit label line just select the same line as the field label In this example 5th line shows the labels for data fields 50 Load and Plot Numerical Log Data Figure 6 4 Field and Unit Labels File Info Data Range Depth Setup Fields Selection Label and Unit Raw Fields Label Line Number Unit Label Line Number File Content 7638 122 334 061005 574 853027 SUR amp 334 0610 2 7477 T 334 2134 2 ATT amp 334 3658 afar 9 334 5182 2 7477 10 334 6706 ddA 11 334 8210 2 2477 12 334 9754 far 13 335 1278 32 7477 l4 335 2802 2 7477 15 335 4326 dA LG 335 5850 2 7477 Lf 335 7374 ATAT i8 135 8895 2 7477 19 336 0422 2 7477 20 336 1946 eae 21 336 9470 2 2477 22 336 4994 fare 23 336 6518 3 75477 24 336 042 2 7477 25 336 956
7. Aini Min Max Type f Caer y Line T Auro Deoynload Images Status After logging in the user interface will display available split core and whole core section images and numerical datasets for plotting To load the available images click on the checkboxes in each section row The client plugin will start downloading and loading the section images in the background and show in the main visualization canvas 79 Corelyzer server and plugin clients Figure 10 3 Main session client plugin user interface ANN 0 5 5 3CelabwaweCorelhzer 0 0 0 0 0 0 0 0 0 Sereer Connection Server i i Correri Logout Loadiog Sane log sp ttures Whole Cores Chan Sections eren Mare ph ime Chu pirg Aral 01 00 1 B_ OOJAIM g 59 3 35 9 69 LH Ye 1 OI 001B OTEAIN 19 55 20 10 19 55 Hi Yen QUI UCIB TIEMAN zU 10 20 45 fo Ye QUI U0IE OTEMN 28 17 25 07 rail LH Yes 001 001E O19AIN 25 12 25 45 ThE Li Yes 901 001B O19AUM 25 09 28 08 53 598 L J Ye QO01 U0IE ONDAN 25 40 27 40 fh 4 I Yes OOI UMILE OZOAIM 27 80 28 15 zT IBI Tea QUI UOLIB O4 LAM 8 28 2000 LITE iB Yes OO1 00 IR OJ15A4N 290 57 29 E 7 IST i Yes 601 0018 02 AUN 50 11 11 11 0 11 Li ur i o01 001B OF 7AUN 51 11 32 11 41 11 iB Yii 001 0008 027AUN 32 11 33 11 k2 11 im ui Dataiets ih wen 7 ami Va Im Density g cc Mucsr le Sos eb ey 15 5 ih Min Max Type Car Lini l Dapy Agely T Aura Deswnilead Images fus Connecr
8. Dynami borehole electri Pass 1 Dynami borehole electri Pass 2 Dynam borehole electri Pass 2 Dynami Open Search Load selected data files Then depending on where do you run the program you can choose to access the on ship version or the Internet version of the service On ship version will use the service provider URL http loa ship iodp tamu edu services http load ship iodp tamu edu services and the Internet version will use the service provider URL http brg ldeo columbia edu http brg ldeo columbia edu services Once the service provider is selected the available site and tool options will be downloaded and populated in the selectable combobox options Or you can also type in interested site and tool and then click on the Search button to search for available data The search result will be shown in the table rows below You can use mouse to highlight multiple rows and click on the Load selected data files button to download and load the data image files 44 Load Images For FMS images since the depth and length information is not directly available Corelyzer will attempt to load these images by guessing from their file name For example a FMS image file named 306 642E p2 D 372 442 gif will be parsed and implies that the FMS image will contain data from 372 to 442 meters Corelyzer will use these 2 values to determine the depth and length of the interval of interest
9. File menu and then select Show IODP lists Then clicking on the Logging DB tab in the popup window as shown in the following figure 56 Load and Plot Numerical Log Data Figure 6 9 Logging DB tab in IODP tables window Section list Affine table Splice table Service provid http brq ideo columbia edu services Site G42E Tool FMS Leg Sine Mele Taal Measurersent Filename 306 B42E FMS borehole electri Pass 1 Dynami 306 B42E FRAG borehole electri Pass 1 Oynam 306 B42E FMS borehole electri Pass 1 Dynam 306 b42E FMS borehole electri Pass 2 Dynam 306 642E FMS borehole electri Pass 1 Static 3 306 G42E FMS borehole electri Pass 1 Static 3 306 B42E FMS borehole electri Pass 1 Static 4 306 642E FMS borehole electri Pass 2 Static 3 306 642E FMS borehole electri Pass 1 Oynam 306 642E FRAG borehole electri Pass 1 Dynam 306 B42E FMS borehole electri Pass 1 Dynam 306 B42E FMS borehole electri Pass 1 Dynami 306 42E FMS borehole electri Pass 1 Dynam 306 G42E FMS borehole electri Pass 1 Dynam 306 B42E FMG borehole electri Pass 1 Dynam 306 B42E FMS borehole electri Pass 1 Dynam 306 642E FMS borehole electri Pass 1 Dynami 306 amp 42E FMS borehole electri Pass 1 Dynami 306 642E FMS borehole electri Pass 1 Dynami 306 B42E FMS borehole electri Pass 1 Dynami 306 642E FMS borehole electri Pass 2 Dynam 306 642E FMS borehole electri Pass 2 Dyn
10. be constituted The Steering Committee will be comprised of key U S IODP and related database e g CHRONOS SedDB developers and users as well as representatives of other core based enterprises e g ANDRILL ICDP LacCore Data will be made available directly from the numerous hard rock and sediment databases or through access provided by a portal such as CHRONOS CoreWall s software displays section images from one or more cores along with discrete data streams and nested images to provide a robust approach to the description of sediment cores Split core surface images are the fundamental template of sediment descriptive work Loaded horizontally and viewed in high resolution along a sliding plane features such as lithologic variation macroscopic grain size variation bioturbation intensity chemical composition and micropaleontology are easier to interpret and annotate In particular the CoreWall Suite will incorporate the new Correlator software the updated version of CLIP e g Sagan and Splicer that was developed by the Lamont group more than 10 years ago into a new portable visualization tool that will work across multiple platforms and interact seamlessly with both JANUS ODP s relational database CHRONOS PetDB SedDB dbSEABED and other databases This functionality will result in a CoreWall Suite module that can be used and distributed anywhere for stratigraphic and age correlation tasks The versatility and flexibility of these enha
11. command java cp CorelyzerSessionServer jar corelyzer plugin andrill CorelyzerSess After running that command you can logout of the server machine and the server program will continue to run To properly shutdown the server use the server shutdown command available to the admin client Running the administration client You can run the admin client from anywhere Simply have the JRE 1 5 or greater and keep a copy of the CorelyzerSessionServer jar file To run the client simply run the command java cp CorelyzerSessionServer jar corelyzer plugin andrill CorelyzerSessionAdmi Where you would replace the I P 192 168 1 1 with the proper hostname or IP of the machine running the server Following is a detailed look at the set of administrator commands Administrator commands Command new section Arguments Section name Starting depth in meters and Length in meters Purpose The main purpose of the command is to notify to the server that a new core sections exists Effectively creating empty slots of split core image and whole core image entries This is also used so that when a new data comes in there are correlations to depth intervals and section names Command new missing section Arguments Section name prefix Starting depth in meters and Length in meters Purpose The main purpose of the command is to notify to the server that a new missing core sections exists Effectively creating empty slots of split
12. core image and whole core image entries Using command like new missing section and001 0 0 1 5 will create a new section with section name and001_0 0 1 5 missing 75 Corelyzer server and plugin clients Command new split core Arguments The URL to the image file The name of the section the image comes from The DPI dots per inch of the image in X horizontal direction and Optional The DPI of the image in Y vertical direction Purpose The purpose of this command is to let the server know the web address of the split core image that was created from the core section This will let the server then notify the clients that the image exists and is available for download and viewing in Corelyzer Command new missing split core Arguments The section name of missing split core Purpose The purpose of this command is to assign a empty split core image to a core section due to there might be no split core image available but users still need to access the data and whole core images The missing section name convention will be like prefix start depth end depth eg and001 186 7 187 5 Command new whole core Arguments The URL to the image file The name of the section the image comes from and The DPI dots per inch of the image Purpose The purpose of this command is to let the server know the web address of the whole core image that was created from the core section This will l
13. in the options below If the Collapse Graphs option is checked all checked graph plots will be fit into a single drawing box Otherwise each graph plot will be shown in individual box row in the main visualization area as shown below 60 Load and Plot Numerical Log Data Figure 6 12 Graph plot without graph collapse Load and Plot Numerical Log Data In some cases you might want to amplify the actual scale of the graph plots when you are looking data plots in great depth range To increase or decrease the graph vertical scale you can first click on the visualization canvas area and then press or to decrease or increase the graph s vertical scale on the screen A screen capture video of these actions can be found in this link online size 2 0MB http www evl uic edu cavern corewall documents movies 6 4 GraphParameters mov 62 Chapter 7 Interactions 7 1 Interaction Scheme Als 7 1 2 The basic interaction scheme is a mouse based interaction The application is best run using a two button mouse with a scroll wheel In the most recent version of Corelyzer the mouse clicks and events are context sensitive This means depending on what your mouse pointing to the response of the application to mouse events can vary Panning To automatically begin panning using the Click and drag style first left click on the visualization window making sure not to click on any objects e g core section i
14. loaded into another newly created track using similar steps To arrange them side by side use keyboard mouse gesture Shift Drag one track away from another in the vertical direction If you need to move individual section along the depth direction you can use Alt Drag gesture to move sections to different depths 12 2 More question More description 89 Appendix A Appendix A 1 Why is the Image DPI Important Corelyzer is a system that intends to bridge core imagery from multiple sources and scale as time moves on and resolution improves To do this the system scales all the images so that these varying resolution imagery can map to a space that will indicate what the dimensions of these images actually represent In other words so that an image of a 1 5 meter section appears to be 1 5 meters in length despite how high of a resolution image you take Does this mean that getting higher resolution imagery is a bad idea No because you can always zoom in to see the finest detail available on the image The higher the resolution the image is i e the higher the DPI then the more details that can be seen A 2 Making Sure the DPI of an Image is Correct Here we will discuss about how to make sure a core image has the correct DPI At this point let s assume that your digital line scanner scans the core at 100 dots per centimeter This is equal to 254 DPI The first thing to do is open the image in a program like Adobe Phot
15. rp PET IDEE 29 5 1 Load Images from local files eee taedet re Ita Re rit p Rel 30 5 2 Load Images from online services sss HH 31 5 3 Load Images from CoreCast syndication feeds cece ce eeceeece ence eeeeeeeeeeeeeeeaees 33 5 3 1 Subscribe to CoreCast feeds 2 0 0 cece o snio s ence ence EE EEE EEE Esie 33 5 3 2 Load core images from CoreCast feeds sess 37 5 4 Load images using IODP formatted section list eses ee eeee een eeneees 40 5 5 Load FMS images from IODP USIO logging database sse 43 6 Load and Plot Numerical Log Data ssssessesseseee ee ee m enm e He mee mener 46 6 1 Native Corelyzer XML Format Dataset Files sese 46 6 2 Use Quick Data Import 2 0 05 ote beer eee qe eese Eee cera e De repe 46 6 3 Use Custom Data Import oer eer de era RR EE Re SORS EE REP ERR RR REREETIR 47 6 3 1 A step by step walkthrough example sse 47 6 4 Download from IODP USIO logging database eH 56 6 5 Plot dataset graph scie Loci eee argen tende dete ve cesta cy eie eint 58 Te Interacuons crror seses tee RC RP IRE ERE DERE RE RE RARE 63 7 1 Interaction Scheme ree Deep e EI ERREUR P METIDES 63 TTL Pannig doce n rote e e e E ted cob ap rre terio bee 63 71 2 ZOOMING oL NR e e rH EIER SSS 63 7 1 3 Siding a section riesen Ie ERR Rr Rt ERR MER 64 iv Corelyzer User s Manual
16. startup script import img cron Sample script that can be placed in crontab to import section image summary report import data cron Sample script that can be placed in crontab to import dataset summary report CRP Dataset summary report example file Notice that img summ Section image summary report example file tab separated fields in each line the data s depth must be within the range of sections existed in server Some notes Convert raw scanned image files from BMP or TIFF to JPEG files to reduce file size and save some network transmission time The server assume the splitcore images are in vertical orientation and it will tell clients to rotate them so images will be layout horizontal way Before import the dataset make sure the data are in the range of sections already available in the server 81 Chapter 11 Fine tune with Correlator 11 1 Before start Download Corrlator and Corelyzer You have to download and install Correlator and Corelyzer The latest version of Correlator can be downloaded from here http sqlcore geo umn edu CoreWallDatabase cwWiki index php Correlator and the latest version of Corelyzer can be downloaded from here http www evl uic edu cavern corewall downloads php 11 2 Interaction flow In the following section we will show step by step how to connect to Corelyzer from Correlator to use available core images assisting choosing tie points in cre
17. 0 0 og 0 0 0 0 HH EG A screen capture video of these actions can be found in this link online size 1 6MB http www evl uic edu cavern corewall documents movies 5 2 LoadJanusImages mov 5 3 Load Images from CoreCast syndication feeds Corelyzer supports core data list syndication CoreCast via Atom feeds If you subscribed to feeds they will be attached to the Subscription label in My Core Repository 5 3 1 Subscribe to CoreCast feeds First show the iCores control window if it is not on the desktop Then click on the plus icon to add a new feed 33 Load Images Figure 5 6 Add a new feed File Edit Shane Plugging Liss Toole Help If you know the feed URL just copy paste the URL string in the popup dialog Otherwise you can click on the Browse button to list available feeds Figure 5 7 Specify feed URL AnA Wares File Edit Share Plugins Ls Tools Help ESI jy Track Sections Dana Files Fields s Here the Browse button is clicked Next click on the Refresh button to show available feeds 34 Load Images Figure 5 8 Refresh available lists Subscribe Check the feeds interested then click on OK to subscribe to selected feeds These feeds will be added to the main iCores control window Click on the feed entries under Subscription label will show the list of core images in the feed Click on a core image entry above will show a summ
18. 07 1H 1 7 6 605 50 131 1427 1 1873 89 2873 155 7109 0 9064 0 08 1H 1 8 6 605 50 130 9736 1 2688 95 0648 166 1739 0 8592 2 41 1H 2 92 6 604 50 130 9019 1 5467 152 7585 202 4669 0 698 2 42 1H 2 93 6 604 50 131 1098 1 5654 152 2331 205 2369 0 6871 2 43 1H 2 94 6 604 50 130 9408 1 6787 148 03 219 8154 0 6214 4 41 2H 2 20 6 605 50 5436 214 1 9546 271 8012 10625 5 0 4614 4 42 2H 2 21 6 605 50 130 9477 2 0751 287 0326 271 77301 0 3915 4 43 2H 2 22 6 606 50 130 9545 1 9434 300 9818 254 4949 0 4679 Each section s name can be composed by prefix GLAD4 HST03 1A with suffix from the string in the SECT NUM column So check the Customize Section Name checkbox with GLAD4 HSTO3 1A section prefix and the number 2 in the Name Column Number will give the sections named GLAD4 HST03 1A 1H 1 GLAD4 HST03 1A 1H 2 and GLAD4 HST03 1A 2H 2 Also notice that you need to use values from multiple columns to compose your full section name you can also fill in string like 2 4 7 to have values from multiple columns in the full section name separated by 52 Load and Plot Numerical Log Data Figure 6 5 Depth setup Fileinfo Data Range Field amp Unit Label Depth Setup Fields Selection Hame and Depth Column Depth Column Number LI SECTION DEPTH i Depth Mode Customize Section Name Section Prefix 7 63B ngt dat Mame Column Number File Content 1 HOLE 763B 2 LEG 122 3 TOP 334 0
19. 1 0 89 horizontal Lng 199 SER 1217 NA C NENNEN i GE NITET NN T RN Ss NN i N A image 5h SUIS E L5 3145 00 0 90 horizontal summa Core Information Summary magr 53 025 E T sd ie ele ag 00 epi 5144 JO erties ja 2 dw 4 3 Visualization canvas This is the main area showing core data visualization 27 Corelyzer Layout Figure 4 5 Visualization canvas with loaded core data A screen capture video of start and quit Corelyzer can be found in this link online size 1 2MB http www evl uic edu cavern corewall documents movies 3 1 StartAndQuit mov 28 Chapter 5 Load Images Corelyzer by default visualizes core imagery by placing the image on a horizontal track A track is just a way of grouping multiple section images Before you can load an image in Corelyzer you must first create a track To create a track you must select the menu File gt Create a Track after which you will be prompted to enter a name for a track Once you do this the Track listbox in the main menu will update Figure 5 1 Create a track File Edit Share Plugins Lists Tools Help Maud kh Cone Biepeergipen Miri Farel Sestian Track Sections Gata Files Fields Li Jubii NETA SAFC ai Leg 199 eiris Leg 199 S1716 Pun Ling 199 Sae be LF Pierre ipa thee track name Tracks are a way of grouping Since we have nothing in our grouping track then nothing in our visualization window wi
20. 6 1005 4 BOTTOM 574 853027 5 DEPTH SGR COR THOR URAN POTA 334 0610 2 7477 2 5013 0 3589 0 0278 0 0747 7 334 2134 SIATS 2 5013 0 3589 0 0278 0 0747 8 334 3658 2AT 2 5013 0 3588 0 0278 0 0747 58334 5182 ILIA 2 5013 0 3589 0 0278 0 0747 10 334 6706 2 7477 2 5013 0 3589 0 0278 0 0747 11334 8230 2 7477 2 5013 0 3589 0 0278 0 0747 12 334 9754 2 7477 2 5013 0 3589 D 0278 0 0747 13 335 1278 2S PATE 2 5013 0 3585 50 0278 0 0747 14 335 2802 2SPATT 2 5013 0 3589 5 0278 0 0747 15 335 4326 2IIATT 2 5013 0 3589 0 0278 0 0747 16 335 5850 IIT 2 5013 0 3589 0 0278 0 0747 17 335 7374 rar 2 5013 0 3589 0 0278 0 0747 18 335 5898 Meri 2 5013 0 3589 0 0278 g 0747 19 336 0422 2 7477 2 5013 0 3589 0 0278 0 0747 20 336 1946 2 7477 2 5013 0 3589 0 0278 0 0747 21 336 3470 27477 2 5013 0 35889 0 0278 0 0747 22 336 4994 2 2477 2 5013 0 3589 0 0278 0 0747 23 336 6518 HIA 2 5013 0 3589 0 0278 0 0747 24 336 8042 2r ArT 2 5013 0 3588 0 0278 0 0747 25 336 9566 IPM 2 5013 0 3589 0 0278 0 0747 26 337 1090 IPM 2 5013 0 3589 0 0278 0 0747 27 337 2614 2 7477 2 5013 0 35869 0 0278 0 0747 28 337 4138 2 7477 2 5013 0 3589 0 0278 0 0747 29 337 5662 SAPE 2 5013 0 3589 O 0278 Ord Gti dtr 2 2 Canes sack In the Fields Selection tab you then can select the data field columns that you want to import into Corelyzer Load and Plot Numerical Log Data Figure 6 6 Fields selection Pick Value Columns File Content The data import process will
21. 6 2 7477 26 137 1090 2 7477 of 337 2014 afar 28 237 4138 2 777 29 337 5652 2 7477 Next depth information parameters have to be specified You have to specify which column means depth In this example the depth is in the first column In the Depth Mode selection you can select from either Section Depth or Accumulated Depth Section Depth means the depth values are measured from the beginning of each section that the data are acquired from Accumulated Depth means the depth is measured from the bottom of the sea lake floor 51 Load and Plot Numerical Log Data Because internally Corelyzer arranges depth values into sections it in one way fits how certain parties obtain the data from sections of cores In the other way it helps renderning performance So if the Customize Section Name is not checked the data will be put into sections suffixed with section numbers automatically If your data files has section information embedded like data files from LacCore repository or you have your own section naming convension you can customize your section names with Section Prefix and Name Column Number For example if you have a data file looks like this Geotek MSCL Version 3 0 GLAD4 HST0O3 1A O0UT created at 12 37 15 on 08 21 2003 SB DEPTH SECT NUM SECT DEPTH ST PWAmp PWVel Denl MS1 m cm cm m s gm cc JSI 0 06 1H 1 6 6 605 50 130 9347 1 2618 82 5908 165 2135 0 8632 0
22. Corelyzer User s Manual Yu Chung Julian Chen julian at evl uic edu Corelyzer User s Manual by Yu Chung Julian Chen Version 4 07 13 2009 Abstract Corelyzer is a scalable extensible visualization tool developed to enhance the study of geological cores The strength of Corelyzer is the ability to display large sets of core imagery with multi sensor logs annotations and plugin supported visuals alongside the core imagery This document describes how to download setup and use the software Table of Contents About CoreWall 2 eth tere Pete ette rex itte es nak so Du TRU se E Rp er de dens ix 1 Pre installation Requirements esses eene hme ee hne ee hne ee hne nenne ee rne 1 1 1 Hardware oic Deere Re Re Er M e IRSE ES ERR Mir AERE SER 1 1 2 Example Hardware Setups ssssssssesssessese eee e menm ene mee mee hen rennen 1 1 2 1 ANDRILL Antarctica Geological Drilling 0 0 0 0 ee 1 1 2 2 Electronic Visualization Laboratory University of Illinois at Chicago 2 1 2 3 National Lacustrine Core Repository University of Minnesota ssss 3 1 2 4 Lamont Doherty Earth Observatory the Earth Institute at Columbia University dsdsidsete abe Da esaet gae POE De tie dan esso o ODE cesis A ous obese oa Be tede tectis ae heise edd 4 IUD EMI 5 2 Download and Install Corelyzer ero ie chere med Rer orte dE E erre ird 7 2 1 Download Corelyze
23. E Leg Site Hoke Core Cove Type Section TopOHfset BotbnomOffser Depth Dara Ron i Data Type Bulk DensitjiG RA Updated Time 2009 01 18 21 15 22 091810 Cenerated By Correlator 2g 1215 A i H 7 0 QC t oe d 0000600 null a x 0 MI 0 090CX 0 A 1314 A H i 5 000004 5 0000 1 050000 i416 A H i 10 056900 10 000000 0 100000 iib A H i 15 0009001 15 000000 0 150000 i4 A H i 20 0008 20 000040 1 2 0006 l4d4 A H i 25 005000 25 000000 0 25 0060 1438 A H i an gatiti 30 000000 1 300060 a A H L 35 00000 35 000000 0 350000 1 433 A H i 40 ood 40 065000 0 400060 1423 A H i 45 004040 45 000000 0 450000 La A H L 50 DODODU 50 060000 0 500008 1 345 A H l 55 00000 55 ROUX 1 550060 1 392 A H I 60 DOO 60 Oso D Gon 1 371 A H l B5 000 55 000000 0 65 O0 1 353 A H l FO GOOD 70 000000 D 200000 Lala A H 1 75 000000 75 000000 0 250000 Lalit A H 1 Bn 005000 80 000000 0 800000 1 417 83 Fine tune with Correlator Figure 11 3 The image list file format loaded in Correlator Data List Generic Dara Duta Files leg site hole core coe Type Section TopOff ses Bottomffset Depth cropped_asmar_id 202 1239 B 0 000000 0 000000 0 000000 tp parm ce iadp tama edu EOBU rerteary asman re seryice egetFile amp catalagName sEXP ZO Poorer 1H1 202 1258 B 1 H 2 D 0009900 0 000000 1 500000 itg purm ce bode tae educ EOB rertearg as man re se
24. LoadNativeData mov 6 2 Use Quick Data Import In many cases numerical data are a list of depth value pairs for a single property Use the Quick Data Import function you can import data files that can be easily edited or generated by external programs like spreadsheet or even raw text data files generated by multiple sensor core loggers The Quick Data Import function will accept plain text files that follows the format described below The plain text file should be in tsv Tab Separated Values or csv Comma Separated Values formats filename ended with csv or tsv The first line of the file will describe the meaning of the values and its contents will also be used for data field labels The rest of the file should be one depth with multiple values per line And example tsv plain text file might look like this values separated by tabs MyDepth Cr Mg FlC200005o00500038S CO 000 10 OU BWNE N m N ws oo To use Quick Data Import select the menu item from the File menu Corelyzer will popup a file selection dialog to select the text file in the format described above A screen capture video of these actions can be found in this link online size 665KB http www evl uic edu cavern corewall documents movies 6 2 LoadDataQuick mov 46 Load and Plot Numerical Log Data 6 3 Use Custom Data Import 6 3 1 In the case your data file is not in Corelyzer dataset XML schema yet you can use the Custo
25. M xi 6 Corelyzer Lopo e iceberg terres EEE K EEEIEE pe dose edente EEEE E EE xi 1 1 ANDRILE CoreWall Set p 5 5 0 rrt rr trei Rer SEEE PEE EEEE EP EPIS SER ede sess ERR rdg 2 1 2 EVE CoreWall Set p nri ru etes qe et dee ite e eee petet e Ee deae s 3 1 3 IzacCor CoreWall Setup 5 5 utto pepe E eO bte tert e ER race geret poa bata 4 1 4 DEO CoreWall Set p utet rnt erre eoe i ee ve eei nete E Pepk SiT 2 1 5 Setup default Java version in Mac OS X sssssssssssseI een aip erriak 6 2 1 Corelyzer Windows Installer secies cece cece cece cece ec HH mee eher 8 2 2 Corelyzer m Mac OS X ieget tse re te Pao deck Rte Exe ERR eSI pae POR DR ER TERRE Re EO TER tS 9 3 1 Display in Control Panel netter edge tese eer tr eesetis decer t ende teste eles 11 32 Display 5 de ege ret e Steves sea oe bays sets PER ERE REEE T 13 3 3 Example desktop configuration sssssessssessee eee em enm eme mee mener 14 3 4 Arrange desktops with drag and drop 00 0 0 eee ee ceee cece cece cece ce eene eens eeneeeneeeeeeeeseeseaeeeaees 15 3 5 Displays setup in System Preferences 2 0 0 0 cece cece cece cc eece eee HH He meme ree 17 3 6 Arrange tab in Displays setting urne er ipis iess Eu PEIC APEN EES PEE ERON heses P Epa 18 3 7 Corelyzer Preferences Window ociscene seei ee Ensen EEEE EEEE eem e He m EEEE ETE A EEEE 19 3 8 Directories preferences 2 netter me eR ERO EE RD Eae E A Pe Ub aeter 20 3 9 Display P
26. The functions listed in the Tool Palette from left to right Interaction mode Normal mode Use drag and drop mouse gesture to pan and the mouse scroll wheel to zoom out the visualization area Create annotation mode Crop a rectangle area to create annotation over loaded core images Modify annotation marker mode Select and highlight a created annotation to modify circled area and the annotation flag icon s position Measure mode To specify the start and end of an interested segment The physical measurement will be calculated based on the mapping information specified in the Display settings of Preferences configuration Cursor type Regular navigation cursor Only the mouse cursor will be shown when moving in the visualization canvas area CrossHair cursor In additional to the mouse cursor a crosshair will be shown when mvoing in the visualization canvas area Common system actions Show Hide main window Show or hide the main iCores control window Minimize Corelyzer Minimize all Corelyzer layout components Quit Corelyzer Close Corelyzer application 4 2 iCores control window The main iCores control window will be used to do major data management and accessing 25 Corelyzer Layout 4 2 1 Menus The menubar has File Edit Share Plugins Lists Tools and Help menus Each menu options will be described in the actions in later chapters 4 2 2 Click on the Local lab
27. Unfortunately there is no way to identify which monitor is represented by which box as you can on Windows You will need to arrange the boxes to match your monitor arrangement You will have to make sure the upper left most monitor in your arrangement will be the main monitor On the Mac the main monitor is visible in the Arrangement tab as the box that contains a white rectangle along the top of the box To designate a different monitor to be the main monitor simply drag the white rectangle to the box that should be the main monitor This white rectangle is actually the menu bar you see on top of your monitor Once the rectangle has been moved the menu bar will also move Figure 3 6 Arrange tab in Displays setting eoo DELL 1703FP lt gt Show all Q To rearrange the displays drag them to the desired position To relocate the menu bar drag it to a different display Menu bar at upper left monitor Mirror Displays Disabled Mirror Displays If you are making a presentation then you may want to mirror your display but normally you don t want to mirror your display so that you will have more screen real estate to view your core images and data 18 Start Corelyzer 3 2 Corelyzer Preferences To start Corelyzer double click on the Corelyzer icon If you start up Corelyzer for the first time a preferences configuration window will show up The window is the Corelyzer Preferences window Using thi
28. ViewSonic LCD Displays Contact Julian Yu Chung Chen lt julian at evl uic edu Pre installation Requirements Figure 1 2 EVL CoreWall Setup 1 2 3 National Lacustrine Core Repository University of Minnesota LacCore s CoreWall Hardware Spec a PC customiz built Reason Athlon 64 X2 Dual Core Processor 4200 2 21GHz 3 25G RAM 1TB HD with NVIDIA GeForce 7900 GTX 512MB RAM 1 30 Dell LCD Display Contact Anders Noren noren021 at umn edu gt Pre installation Requirements Figure 1 3 LacCore CoreWall Setup 1 2 4 Lamont Doherty Earth Observatory the Earth Institute at Columbia University LDEO s CoreWall Hardware Spec a Mac Pro with 4 nVidia GeForce 7300 GT graphics cards 6 Apple 23 Cinema Displays More Information http corelyzer blogspot com 2007 10 1deo corewall setup details html Contact Sean Higgins sean at ldeo columbia edu gt Pre installation Requirements Figure 1 4 LDEO CoreWall Setup 1 3 Software Corelyzer starting from version 0 6 makes use of the Java Runtime Environment JRE The current version of Corelyzer requires Java Runtime Environment above version 1 5 0 Please make sure to install Java 1 5 For Microsoft Windows users Corelyzer will bundle a copy of JRE within the downloaded package You should not have to install JRE separately For Mac users in the current Mac OS X Leopard Java is bundled with the operating system In some cases of Mac OS X Tiger
29. al Lacustrine Core Repository at University of Minnesota Electronic Visualization Laboratory University of Illinois at Chicago Corelyzer is being developed by the University of Illinois at Chicago s Electronic Visualization Laboratory with funding provided by the National Science Foundation under the agreement number OCE 0602121 1X About CoreWall Figure 1 National Science Foundation Logo Figure 2 Electronic Visualization Laboratory Logo electronic e V visualization laboratory Figure 3 LacCore Logo OOOQ0 909006 Figure 4 Borehole Research Group LDEO Logo About CoreWall Figure 5 CoreWall Logo cfe LL Figure 6 Corelyzer Logo xi Chapter 1 Pre installation Requirements 1 1 Hardware Corelyzer takes advantage of hardware accelerated graphics While a primarily 2D visualization program Corelyzer uses OpenGL to accelerate the rendering and take advantage of modern day graphics boards This does mean that the performance of the application is not only dependent on the speed of your CPU but also the power of your Graphics Processing Unit GPU Any modern day graphics card that can run video games from a few years back can easily run Corelyzer Currently the leaders in graphics card technologies are Nvidia and ATI Corelyzer can use lots of hard drive space and main memory It is recommended to have at least 2GB of RAM on your machine if you intend on looking at a hundred meters of
30. alue Columns From previous inputs the field labels will be identified Then you can check which fields do you want to select to the final dataset file A step by step walkthrough example Next is a step by step walkthrough example The example source data file is downloaded from IODP Log database at Lamont Doherty Earth Observatory Columbia University http iodp ldeo columbia edu DATAJ The data file used in this example is 763B ngt dat attachments 763B ngt dat The resulting Corelyzer dataset file is output data xml attachments 764B ngt xml Select the Custom Data Import from the File menu 47 Load and Plot Numerical Log Data Figure 6 1 Select Custom Data Import File Edit Share Plugins Lists Tools Help Create a Session HN 5tatus Create a Track T i Open Image Files 30M E Main Panel Open Dataset Files HO Session Track Sections Data Files Fie Quick Data Import Open a Session File 360 Recent Sessions Save 365 Save Session As HA Core Archive DIS D LIMS D Export Sheets Quit xo The selected file will be loaded into Plain Text Data Import dialog The upper half of the dialog shows different data format parameters in tabs The lower half shows the content of the text file with line number attached to the beginning of each line In the File Info tab the selected file will be shown and you have to select from one of the available separator comma ta
31. am mr RADE EM harnhnla alartri Baer Pema Data files Then depending on where do you run the program you can choose to access the on ship version or the Internet version of the service On ship version will use the service provider URL http loa ship iodp tamu edu services http load ship iodp tamu edu services and the Internet version will use the service provider URL http brg ldeo columbia edu Once the service provider is selected the available site and tool options will be downloaded and populated in the selectable combobox options Or you can also type in interested site and tool and then click on the Search button to search for available data The search result will be shown in the table rows below You can use mouse to highlight multiple rows and click on the Load selected data files button to download convert and load the data files Then follow the Plot dataset graph steps to show data plots of these loaded data files 57 Load and Plot Numerical Log Data A screen capture video of these actions can be found in this link online size 6MB in 1920x1200 resolution http www ev uic edu cavern corewall documents movies LoadFromLoggingDB mov 6 5 Plot dataset graph If you have dataset files loaded and tracks created your main iCores control window should like the following screenshot Figure 6 10 Main window with dataset loaded File Edit Share Plugins Lists Tools Help Statu
32. ary report of the image at the panel below Project Source oooga Title For test only AND1 1A Hole ANDRILL SMS Project Fastest ANDRILL MIS Project Mirrored SAFOD holeG Earthscope SAFOD Current IODP Leg 199 Site 1215 IODP Leg 199 Site 1216 IODP Leg 199 Site 1217 IODP Leg 199 site 1218 IODP Leg 199 Sire 1219 IODP Leg 199 Site 1220 IODP Leg 1995 Site 1256 35 http www evl uic edu cavern corewall iCares feeds subscription URL http www e http sms ar http corewa http corewa http corewa http corewa http corewa http corewa http corewa http corewa http corewa http corewa Load Images Figure 5 9 Select to subscribe feeds File Edit Share Plugins Lists Tools My Core Repository Local Subscriptions SAFOD holeG Leg 199 Sitel215 Leg 199 5ite1216 Leg 195 5ite1256 Help Status Status Type Title De Downloaded image 55 5025 1 E 1 31 Downloaded image 55 5025 1E 1 31 Downloaded image 55 5025 1E 1 31 M A image 55 5025 LE 1 31 r SUM Core Information Summary Image 55 5025 G_i lJjpg split core image 89 depth 4185 SAFOD split core images for holeG 88 5025 1 G 1 1 Ljpg 36 Load Images 5 3 2 Load core images from CoreCast feeds Select one or more interested core images and use mouse right click to see available options 37 Load Images Figure 5 10 Select core image entries and
33. ating affine tables 11 2 1 Start Corelyzer Double click on the Corelyzer icon to start Corelyzer You might want to properly setup the visualization area of Corelyzer if you do not want it overlaps with Correlator s data plot window Please refer to Corelyzer Display Configuration section for setting up Corelyzer visualization area 11 2 2 Start Correlator Double click on the Correlator icon to start Correlator Please refer to Correlator documentation for start using Correlator 11 2 3 Load log data tables and image list table Before using the fine tune function you have to make sure you have loaded both the data table and the image table of the cores Please refer to Correlator document on How to load data files into Correlator Data Manager In the following example 3 data files Bulk Density GRA and a image list data file are loaded into Correlator s Data Manager 82 Fine tune with Correlator Figure 11 1 Example data and image list files are loaded in Data Manager in Correlator iaaii Genere Dara Dara File Dana Enable Decimabe Min Max Upsfated Time z A DENSITY BULK CGRA Enable D 17 1 95 2009 01 18 21 18 E DENSITY BULK GRA Enable 18 1 97 2009 01 18 21 18 c DENSITY BULK CGRA Enable 1 2 1 98 2009 01 18 21 18 Dewenieode Log Data bmage Data Table IMACE Enable 2009 01 28 14 28 Saved Tables Stratigraphy Gata List Generi Dara Data fie
34. b or space In the this example tab separator is selected 48 Load and Plot Numerical Log Data Figure 6 2 Data import file info Field amp Unit Label Fields Selection Data Range Input file name and field separator Depth Setup 763B ngt dat Field separator Lineynumber File T63B 122 334 061005 574 853027 SOR COR THOR URAN POTA 34 0610 2 7477 2 5013 0 3589 0 0278 0 0747 FALETI 2 5013 0 3589 0 0278 0 0747 34 3658 2 7477 2 5013 0 3589 0 0278 0 0747 2 7477 2 5013 0 3589 0 0278 0 0747 34 6706 2 7477 2 5013 0 3589 0 0278 0 0747 34 8230 fran 2 5013 0 3589 0 0278 Moray FAE EFI 2 5013 0 3589 0 0278 ere re 35 1278 2 7477 2 5013 0 3589 0 0278 0 0747 2 7477 2 5013 0 3589 0 0278 0 0747 35 4326 2 7477 2 5013 0 3589 0 0278 0 0747 35 5850 2 7477 2 5013 0 3589 00278 0 0747 2 P T 2 5013 0 3589 0 0278 Morey 35 8898 2 P ATT 2 5013 0 3589 0 0278 Mora 2 7477 2 5013 0 3589 0 0278 0 0747 135 1946 2 7477 3 5013 0 3589 0 0278 0 0747 36 3470 2 7477 2 5013 0 3589 0 0278 0 0747 36 4904 2 7477 2 5013 0 3589 0 0278 Moray 36 6518 2 P T 2 5013 0 3589 0 0278 0 0747 27AT 2 5013 0 3589 0 0278 0 0747 36 9566 2 7477 2 5013 0 3589 0 0278 0 0747 37 1090 2 7477 3 5013 0 3589 0 0278 0 0747 FI 2 7477 2 5013 0 3589 0 0278 0 0747 37 4138 2 7477 2 5013 0 3589 0 0278 O 07AT 29837 5662 2 7477 2 5013 0 3589 0 0278 0 0747 B 4 ok CC B NM D zd Because some text files will have certain number of comments li
35. e adjusted The boxes with numbers represent your monitors that you have connected to your machine If you have a monitor that is not displaying your desktop then it will show up as a slightly grayed out box which is a visual description that says this monitor is disabled If the box indicates the monitor is disabled and you click on the box you will be able to modify the options for that monitor To enabled the monitor make sure that the check box next to Extend my desktop is checked Do this for all the monitors you would like to use presumably all of them Once you have done that click on the Apply button If you did this correctly you will have your desktop visible on all the monitors 12 Start Corelyzer Figure 3 2 Display acini uie Oh the piae TE Di pour onde Woperc left FF Ute thie device at the prrmang montre WI Ester py Wires ekle onde Pera acre Los j ce Start Corelyzer Note Some monitors need to be turned off and on again to realize that they are enabled by Windows Now that the desktops are visible on your monitors you will need to set the display resolution for all of the monitors Corelyzer requires that you set your display settings so that all the monitorss will have the same resolution Example resolutions are 1280x1024 and 1600x1200 There is a slider on your display settings dialog to modify the resolution Once set for all monitors click on the Apply button again If you are prompted to restart
36. ed 10 7 Example dataset file The basic formatting of this file is simple The first row will contain unique column headers that are tab delimited i e separated by tabs The first column of the data by default is assumed to be the column that contains the depth reference for the data in the row Every row of data is also tab delimited and must contain the same number of tabs as the header row in order to positively determine which data value belongs to which column Microsoft amp Excel can export a worksheet as a tab delimited file in the same way An empty entry is considered to be two consecutive tabs and will be dealt with properly Any data that appears to be invalid should be deleted in your spreadsheet program of choice to create an empty entry Depth m Porosity vol WBD g ccm Sus units 12 250 0 454 1 937 241 46 12 270 245 60 12 290 0 420 1 995 244 68 80 Corelyzer server and plugin clients 10 8 10 9 12 310 0 408 2 015 257 45 12 330 0 365 2 087 280 15 12 350 0 387 2 050 305 97 12 370 0 383 2 057 390 86 12 390 0 434 1 971 620 38 12 410 0 282 2 226 762 53 12 430 0 376 2 069 644 55 12 450 0 441 1 959 435 98 NOTE In this example you can see that on the third row there are two blank entries for both Porosity and WBD columns Handy scripts Table 10 2 Handy scripts Script name Function description startserver sh Server startup script adminlogin sh Interactive administrator client
37. eeu or gees 64 7 2 Adjust graph pl t Propertie Sissener En oC t och eU o ee ea eet e ERSE 66 8 1 Annotations for Core Images 93 oi oie eset e desee ed eed t dan eode adeo dd 67 8 2 Select create annotation mode eect e cence ceca cena cen enm eme mene en E he mee eere 67 8 3 Select annotation type docere see Dee peeves URE PH MPO ERE Re Eee de equ Y OR Pepe teases ERN qEE Pe MEUSE 68 8 4 Review and edit a freeform annotation sssssessseeseeeee eee enhn hene hene 69 8 5 Modify annotation marker mode nsee ese eiea ea eem HI aaea 69 8 6 Modify region of interest and marker position ssssssesssee m eee 70 8 7 Enable MEasure mode ov sun ess oe eer eser iet Pe gre t qee eo Pere edo oe greeted es seen 71 8 8 Show measurmp histOry ode eee oe e ee eco vei Ven e rA D Mere ON 71 8 9 Measure on IMA SES su ioi pede see sd dei bos pete leet ei een dude e NEN 72 10 1 Activate chent plugin EHE EIER En 78 10 2 Connect 10 SESSION SEE VOE ihessi na ek zoe i Ep eere EET OPE Pete MERI eR be Pr Here by NP REP tues 79 10 3 Main session client plugin user interface sssssesseee Here 80 11 1 Example data and image list files are loaded in Data Manager in Correlator 83 11 2 The log data file format loaded in Correlator sessee 83 11 3 The image list file format loaded in Correlator ss teen sean eeaes 84 11 4 Right click on the data entrie
38. el in the My Core Repository panel will show the main panel that contains current loaded Session Track Sections Data Files and Data Fields In current hierarchy architecture Corelyzer can have multiple sessions Each session can have multiple tracks and data files Each track can have multiple sections and each data files could have more than one data fields Figure 4 3 iCores control window Local status File Edit Share Plugins List Tooli Help T Sub etes SAFO ail Lig L09 Spe be bs Leg 199 m1210 Leg L99 5861217 4 2 3 Subscriptions Corelyzer supports core data list syndication CoreCast via Atom feeds If you subscribed to feeds they will be attached to the Subscription label in My Core Repository Click on the subscribed feed entry Sranees Main Panel Session Teak Sections A cLapa Hsro3 1 CLAD HSTOS Css will show the core summary in the right hand panel Dara Files GLADA HSTO3 7 GLAM HSTU3 Fields Er Pwamp Pel Deni Ws imp FF 26 Corelyzer Layout Figure 4 4 iCores feed window File Edit Share Plugins Liss Tool Help Py Core Repos tty cre st 2 Local QO ooo I T Vu ries ESE 1 0 Type Trie Dep Leregth Drenten NIA image S SOZS 1 E 11 3141 43 0 90 horizontal T MES LET AQ ERSEMIESA DONA image 55 5025 1 E 1 2 3142 33 0 88 horizontal Oo Leg 199 SRE121B tara m 55 025 LE 13 3143 2
39. ely it seems that most of the scanners don t save off the correct DPI There is a quick and dirty way of checking and making sure the DPI is correct in the section Making Sure the DPI of an Image is Correct Or in the image loading dialog below you can also specify the core section image s length the DPI values will be calculated by Corelyzer 29 Load Images 5 1 Load Images from local files So now we will assume that the images are Horizontally oriented Have an increasing depth from left to right Have the correct dots per inch DPI To bring up the file selection dialog to tell Corelyzer which images to load we need to first select the grouping track in the track list and then select the menu item File gt Open Image Files The Load Images dialog will pop up and allow you to load the section images with properties like orientation vertical or horizontal length DPI and starting depth in meters of the section image etc The upper right of the dialog is an Excel like table Click on the Select Image Files button to fill the table with core section images You can double click each cell to make individual modifications Press Enter when you finish editing a cell Note that if you leave the DPI X and DPI Y value as 0 the length value will be used with image dimensions to calculate DPI values Also you can enable the Batch input checkbox to fill the table parameters You can select orientation length
40. erences JACO 0 mima 00000 0 0 0 0 B Auto check version in sabes B Lock core section image LI use Quaqua E Double dirks 10 zem io section FS Graph aio scale B Annotation icon saio scale Ll Show orsgin axis B Show section labels Camas Always at Below C Depth scrall in vertical depth mode Horizontal Depth 7 Vertical Depth a Canvas bhaciegrund cales j Caras Grid 7 Show Grid Grid Type Basic Cross W Coler Grid Space 18 cm Thickness 1 Hep Camel f 22 Start Corelyzer 3 2 4 Session Sharing and DIS Preferences These 2 preference tabs customize functions for session sharing and default annotation dictionary definition You can use the default values 23 Chapter 4 Corelyzer Layout Once OK button is clicked in the initial preferences configuration a window or multiple windows will be created according to your configuration for the visualization display Figure 4 1 Initial Corelyzer screen Lam And main Corelyzer layout can be divided in the following sections 1 Tools palette 2 iCores control window 3 Visualization canvas 24 Corelyzer Layout 4 1 Tools Palette Figure 4 2 Tool Palette Functions Rios hie lsi EIX Help Tool Palette contains often used functions and modes In multiple monitors setup the Tool Palette will follow the cursor moving from one monitor to another
41. erly shutdown 10 5 Admin commands reference table Table 10 1 Commands reference table Command Arguments new section section name depth in mbsflength in meter new split core image url section name image dpi new whole core image url section name image dpi new dataset dataset file dataset name list sections list datasets list tables dataset name list table data dataset name table name run backup run script script file logout server shutdown 10 6 Client plugin in Corelyzer In the client side a client plugin is provided in Corelyzer software To activate the client user interface select Collaborative Corelyzer from the Plugins menu 77 Corelyzer server and plugin clients Figure 10 1 Activate client plugin File Edit Share Lists Tools Help Janus via Chronos Collaborative Corehyzer iCores Subscriptions SAFOD Poleg SAFOD all Leg 199 Sie 1215 Leg 199 11216 To connect to the session server you can either select or type in the server name from the drop down menu on the top of the client plugin user interface and click on the Connect button The interface then will prompt to ask for the user name and password for accessing the server 78 Corelyzer server and plugin clients Figure 10 2 Connect to session server Serwer Connection Server Co Croda Ceon Whole Coes Chats Depth imi Eun play
42. et the server then notify the clients that the image exists and is available for download and viewing in Corelyzer Command new dataset Arguments Data file to parse and The name of the dataset to append overwrite Purpose This command will parse a tab delimited data file and feed the server new data tables The tab delimited data file must follow the formatting exampled in Appendix B This command will retrieve a listing of sections to use the depth and length of the sections to determine how to partition the data file into tables Once the tables are created the tables are sent to the server and stored in a file with the following name convention dataset section name dataset name gt tab If the dataset name does not exist in the server it will be created automatically If the name exists then the files created on the server will automatically be appended NOTE Existing files will be overwritten automatically If this is an undesired effect please make sure that there are no rows that contain depths of sections that would previously had a table made for them for the dataset If you are only appending to a single tab delimited file without changing previous rows then the overwrite will effectively be doing nothing for previously created tables Command list sections Arguments None Purpose The purpose of this command is to list the existing sections known to the server Returned is a listing of section names the
43. f the graph plots when you are looking data plots in great depth range To increase or decrease the graph vertical scale you can first click on the visualization canvas area and then press or to decrease or increase the graph s vertical scale on the screen Graph plot properties colors To modify the color of a graph first select the Color button on the dialog At this point a color selection dialog will open up Select the desired color and press OK The color of the graph will immediately change The change the color of all the graphs of the same field along a single track make sure that the Apply to whole track checkbox is enabled and click on the Apply button 65 Interactions Figure 7 2 Adjust graph plot properties i pm M ou 66 Chapter 8 Annotation Annotations are currently shown using a marker along the top of a core The marker is a simple interactive visual to indicate that an annotation exists Different markers can mean different types of annotations Annotations types will be added as development continues Figure 8 1 Annotations for core images 8 1 Creating new annotations Currently text and image annotations are supported Annotations come in the form of HTML and property list XML files First an image must be loaded A user can then select Create annotation mode to start creating annotations Figure 8 2 Select create annotation mode s e e EX Create anno
44. file then the fields will show up as selectable items as seen in the image Otherwise the listing of fields will be empty At this point simply click on the check boxes of the fields you would like to be drawn for the section If you would like all the images on a track to display the same fields just make sure that the Apply to all sections in this dataset checkbox is enabled If you do not have pre defined section imagery available you can still plot the dataset with the independent graph feature To do so after you load the dataset files and it is shown in the Dataset list right click on the dataset file that you want to plot select Graph the similar graph dialog will show up and the heuristic graph section will be created and plot the graph in visualization screen s Notice that you will need to create at least a track for it as shown in the last chapter Graph plot properties scaling The three properties of a graph that can be changed are minimum value maximum value and the color The minimum and maximum displayed values can be modified This will take affect after you hit the Apply button If you have the Apply to whole track checkbox enabled all the sections on the track will have their minimum and maximum values modified This is how you can make sure that the scales of all the graphs for a particular field are the same along a whole track In some cases you might want to amplify the actual scale o
45. high resolution core images or more One more thing to note is that Corelyzer does not currently have any mechanisms to support heterogeneous display settings This means that if you have a monitor that only goes up to 1280x1024 and another at 1600x1200 you will have to choose one or the other when setting up your Corelyzer display settings when running the application 1 2 Example Hardware Setups The key for CoreWall is large screens and a good graphics card We would suggest eith the Dell or Apple 30 LCD monitors And in order to drive each 30 monitor you will need graphics cards with a dual link DVI port If you intend to use 2 30 monitors then you will need dual dual link ports Possible selections but may not limite to are ATI Radeon X1900 XT and NVIDIA Quadro FX 4500 cards Following are some CoreWall setups out there Each contact is listed If you need more information please contact each indiviuals or Julian Yu Chung Chen julian at evl uic edu gt ANDRILL Antarctica Geological Drilling ANDRILL s CoreWall Hardware Spec an Apple Mac Pro with nVidia Quadro FX 4500 graphics card 2 30 Apple Cinema Displays Contact Josh Reed jareed at andrill org 1 2 1 Pre installation Requirements Figure 1 1 ANDRILL CoreWall Setup 1 2 2 Electronic Visualization Laboratory University of Illinois at Chicago EVL s CoreWall Hardware Spec a Dell Pentium 4 XPS PC with 3 PCI nVidia Quadro FX500 graphics cards 5 20
46. ieve the high resolution core section images In current version Corelyzer supports 3 online core image services JANUS database with CHRONOS service IODP LIMS on shore database and IODP LIMS on ship database For 2 IODP LIMS services the query web service protocol was used to retrieve core image s metadata Corelyzer uses the CHRONOS webservices capabilities to access JANUS and retrieve the URLs to the images Corelyzer will rotate the images 90 degrees counter clockwise because all the IODP images are vertically oriented where Corelyzer displays data horizontally This plugin accuratly position the core sections using CHRONOS web service to access the curated length and top depth mbsf of each core section image The user interface has been designed in a stream lined manner To bring up the plugin select the menu item File gt Show IODP lists gt Image list from services tab Here are the steps to get image listing and load selected images 1 Select which online service to use Currently CHRONOS on shore LIMS and on ship LIMS services are available 31 Load Images 2 Enter an IODP site to search for e g site number 1215 3 Click on the Search button A listing of core section images should become available 4 You can optionally input the depth range to filter the returned available image section in the result table Depth range should be input as string like 0 20 meaning only list image section of top depth from 0
47. installation Java 1 4 might be still presented in the system In that case you will have to modify the default version to version 1 5 Pre installation Requirements Figure 1 5 Setup default Java version in Mac OS X aan G Applications Bg Developer ll Groups lU Library B System G Users T TY T T F C ava Wb QuickTime Broadcaster gt E Directory Utility A Input Met C QuickTime Player amp Disk Utility E Java Prefe BR amp Grab fs Java Web TA Remote Desktop iw Grapher ie Remate De onnection ag iPhone Ca tiom Utility l 6 Safari Java B3 Server B Keychain Access iiS Snapz Pro X KM Migration Assistant BB Spaces Network Utility c Stickies Hi ODEC Administrator E System Preferences B Podcast Capture Ty TextEdit H RAID Utility Time Machine amp Remote Install Mac OS X E Utilities System Profiler Gh VMware Fusion BE Terminal lt gt VPNClient a VoiceOver Utility 5 B3 Wacom Tablet X X11 ki il WireTan Pro k ll ES Xserve RAID Update k ll E Mac E Applications 39 Utilities 3 Java 0S Java Preferences LAGO Java Preferences Java applet versions J25E 5 0 32 bit Web browsers use this onder to determin J2SE 1 4 2 32 bit the java Virtual Machine to use far applet first compatible architecture in this list Restore Defaults Drag to change the preferred version Java application versions J25E 5 0 3z bu java applications Web Sta
48. ir depth and length in meters The output is displayed to the command line Command list datasets Arugments None Purpose The purpose of this command is to display datasets known to the server Displayed are the names of the datasets followed by the attributes in the dataset and their respective minimum and maximum values within the whole dataset Command list tables Arguments The name of the dataset 76 Corelyzer server and plugin clients Purpose This command will display a listing of tables within a given dataset This is useful if you do not know if a given section is covered by a dataset because the names of the tables are the names of the sections Command list table data Arguments The name of the dataset and The name of the section table to view Purpose This command will display the data of a table from a given dataset The data is displayed in a tab delimited form with the first line as the header followed by lines of numerical values Table cells that are invalid will appear blank Command run backup Arguments None Purpose The server runs backups automatically if the last backup has occurred more than 24 hours ago This command forces the current day s backup to occur Command logout Arguments None Purpose This command allows the administrator to logout and ends the client program Command server shutdown Arguments None Purpose This command allows the server to prop
49. l hard disk 68 Annotation Figure 8 4 Review and edit a freeform annotation P n0 nn Annetatien by ulea og 01 2007 an 02 44 25 CST OO Caen Da 01 22 07 m 0332 02 CST julian wro best bext Um DI Z2 07 af 03 32 8B CST julian wr te s ERA Un DI ZZ OT at O3X GDZ CST julian wrote vest attache ATbacherse nt Ana paaa CB Aa arry hare E raie Cane p Ok iima ieh Cie UNDIFMTO Open is Browser Any time after the marker is created the user can change to marker manipulation mode by clicking icon at the toolbox in the upper left screen Next select the marker icon and then by click and drag the green box to change the region of interest Figure 8 5 Modify annotation marker mode mep he Ex Modify annotation marker mode Help 69 Annotation Figure 8 6 Modify region of interest and marker position A screen capture video of these actions can be found in this link online size 14 0MB http www evl uic edu cavern corewall documents movies 8 CreateModAnnotation mov 8 3 Measuring Mode Switch to measuring mode by click the measurement icon in the toolbox at the upper left corner To measure click two points on the visualization screen the physical length measurement will be calculated and saved to measuring history The last value will also be copied to system s clipboard so you can easily paste to other applications or the annotation 70
50. ll change Now we add images so that way we can see something and have something to interact with First let s remember that our track is a horizontally oriented track with an increasing depth as we go from left to right This means we will need images that are horizontally oriented in such a way that they are increasing in depth from left to right IODP images are vertical with increasing depth as you go from top to bottom Fortunately we have created a Corelyzer Plugin that makes use of CHRONOS webservices to access the JANUS database The plugin is called the Chronos Janus Plugin and will be discussed later For now we will assume that there are some images of core sections that are horizontally oriented with an increasing depth from left to right If you know the images orientation you can also specify that individually in the image loading dialog shown below We also have to make sure that your images have the correct dots per inch DPI Why does the DPI of the image matter This is discussed in detail in the appendix It basically establish the correct mapping between the image dimension to the physical core dimensions How do you know what is the right DPI of your image This all depends on the equipment in which the image was retrieved Usually most line scan cameras that are manufactured for the creations of high resolution digital line scan images of core sections have this indicated in the advertisements of the scanner Unfortunat
51. m Data Import feature under File menu to specify few parameters and have the program to convert your data file into Corelyzer dataset XML format A user can convert a plain text tabular data file or a Geotek generated data after pre processing and data cleaning to Corelyzer XML data format and directly imported into Corelyzer working session Import parameters File name Original input file name Use File button to select your input file Field Separator Input what is used to separate each fields in the input file Commonly used separator might be comma for CSV file Or Tab type in X delimited file Section Prefix The prefix used for naming each section Start Line Number In the input file the starting line number of data values starting from 1 End Line Number In the input file the ending line number of data values Fields Label Line Number What is the line number for labels of each value in columns Unit Label Line Number What is the line number for units of each value in columns If there is no such line just input the same line number as Field Label Line Number Name Column Number Which column field should be picked used as the name of section The final section name will be composed with Section Prefix and Name Column Number A simple comma separated expression is allowed to compose the section name Depth Column Number Which column will be treated as depth values Column index starts with 1 Select V
52. mage files m s Uo Us UD UD Je je EEE EE EE EE EF EF EE OU UE Ree dai dad eee gom gon Gom aum ETEEEREEETRERETETETETETE TY V NT T S zb omm de dui Bei nm Fui onm QA d M LA de tni Rs nme ag Uh A Je ds By oan 32 Load Images Figure 5 5 Online core image service query Logging DE Aie table Salice cable Sarees prercidier thos Fwebeerv iodp tamu edu BOBO Site i330 Depth Filter im 0 20 vr IT XroT 3T IT XroT 3T IT Xr8oT 3roT 3XroT x IT Search results ld XroT IT XroT OT IT 3T Sane EEN EE EET EEN EEN EE UL330 L330 Uv1 3 UL330 L330 WL330 UL330 WL330 UL330 UL330 UL330 WL330 Ub Ui Ub RE DU UB KD QD DP UD VDO UD UR UD VEO DO VEO h MAR Ld L Fu Kg Ku Mg Kd Bg Mu K Pe Pe p ee de dem dem Ei a i m jt oo 55 oo a0 LE LE a0 LE E E LE 0 0 5 ad a0 B ad a0 m wo OE Dra cm deu f n m je ur en ZEETFTTTFTTETTTZLTZITZE Load selected image files Sector Teo Bema oo 0 0 6 0 0 0 0 0 iki b 0 0 Liki oo o 0 Liki 0 0 0 0 oo 0 0 imh oo oo i5 3 8 435 Gal ET as JET 11 15 12 63 14 11 15 1 15 34 16 2 17 66 13 12 oo 1 amp 1 amp 1 amp Lo 6 909 b r60 1 4BD 1 489 1 479 140 1 479 D 9590 b B9 D z60 1 459 1 amp BD 1 459 un LI Oo oo Limi Oo Limi oo 0 0 g gg 0 0 ag
53. mages sss 39 5 12 Images loaded with iCores feeds sssssssssssessese em mH en mere 40 5 13 Select load section list in IODP menu sss meer 41 5 14 Select sections and load images sssssssssssesse ee e Hem Hem emere 42 5 15 Logging DB tab in IODP tables window sss eee 44 6 1 Select Custom Data Import ison estoe aere a E E III eI meme menie entren 48 6 2 Data import file 1nfo oret e et ere E Ree erect re Ere tte Pee e Se Re ee vents 49 6 3 Data ran ge tab eere tee dee ee bep rese rtt oreet eve der Rose ete eese PE Re Sie RO does 50 64 Field and Unit Labels re ertet rr de mtr pr Pere Prae Ere Pe iae oin agree 51 6 5 Depth setup i isse ee ERR REDE PRIURMENI EARUM UII TUE 53 6 6 Fields selection 5 cre rtt tpe e E needa da ette E ex eines sa Pd T Ee et RE E EAS 54 6 7 Save converted file 3 jest neue e te Rer erre bee E IEEE ese e epe eee peo TEA 55 6 8 Create a track for data graph plot echter pecore reir Rep Rp 56 vi Corelyzer User s Manual 6 9 Logging DB tab in IODP tables window see 57 6 10 Main window with dataset loaded ssssse Hee 58 6 1 Graph dialog co icect e estre tti e Eee ee tog R MR dyn cue lee Pope ive onto Deed qucd 59 6 12 Graph plot without graph collapse 2 2 0 0 cece cece cece cnec cece m mH Heer 61 7 1 Jump to depth dialog 4 estote ere eee ree deeds setveesdehesecensteades tees
54. mages graphs annotation markers etc If you successfully clicked and are in the panning mode then the mouse pointer should change In Windows it will likely change to a four direction pointer On Mac OS X it will change from a black mouse to a white mouse cursor To pan keep holding down the left mouse button and drag the mouse to move the view of the scene Zooming If you have a mouse wheel zooming is as easy as scrolling the wheel back to zoom out and forward to Zoom in Assuming a particular area is of interest and you want to zoom in on it simply point at that area of interest and use the mouse wheel to zoom in The area will stay in the same place as the scene changes in scale Similarly you can zoom out to see more of the context that surrounds a particular area You can also use keyboard for navigation in Corelyzer You can use the four direction arrow key to pan around the main visualization area To zoom in and out around the mouse cursor position you can press the and keys If you want to jump to a certain depth directly first click on the main visualization area and then press the j key to bring up the Jump to dialog Input the depth in meter and the main visualization area will jump to designated depth directly 63 Interactions Figure 7 1 Jump to depth dialog Please input a depth value in meters Cancel jJ oK 7 1 3 Sliding a section To slide a section image first left click
55. meter to 20 meters mbsf The default value 0 0 will list all image sections returned by the online service 5 Select the images to load 6 Click on the Load selected image files button 7 User must wait as image files are retrieved over the web processed and displayed A progress bar indicating the status will update during the process in the main window Each loaded image will be loaded and placed in the seesion and track named with the combination of leg site hole and core metadata information from the online core image server Figure 5 4 Online core image service query interface J image Lge from file Legging DB Alfime table Selice table 1218 la a EEE EEE ua be ee ae Tye been ee ee er ib 1218 t 05 15 Pee itb 3121E amp 5 65 Ls E15 Bee ve 121 oo 66 3 E5 Bee ib 1218 B 060 45 15 154 ih OUP ao oo amp iI Bee jb Urs os 65 FS 5b J sb 01218 os 60 oO kis 254 ve Oe oo 065 X2 E15 Bea 195 1218 os 060 7 L5 25 199 121 amp B 60 112 IS 254 ive 1215 amp 5 605 4127 L5 254 199 1218 GG 00 142 L5 25 199 1215 B 60 157 IS 54 159 1218 amp 5 60 172 i55 254 199 1218 oc 60 1746 i4 254 199 121 amp B oo 177 L5 54 139 1218 amp 5 60 12 L5 254 139 1218 oo 00 L5 254 199 121 amp oo 00 Ls LS 254 139 1218 ad o 3 O68 ree 1339 1218 Q0 00 158 als jm ly 1215 Oo 0 0 3 9 1 5 red ET ETT ET Aa ca LE Ted Open Load selected i
56. n image stationary user can not move it to arbitrary depths Use Quaqua if the program will use Quaqua library to make the user interface components more Mac like only for Mac Double clicks to zoom to section if zoom in out with double click Graph auto scale if the plotting graphs automatically scale during zoom in and zoom out Annotation icon auto scale if the annotation icons automatically scale during zoom in and zoom out 21 Start Corelyzer Show origin axis if show the visualization origin axis Show section labels if show the section label if no images are available with loaded graphs Canvas Always Below if the visualization area always below all external applications on the desktop Depth scroll in vertical depth mode if the mouse wheel action interpreted as scroll along the depth instead of default zoom in out action when the depth mode is set to vertical Horizontal or Vertical Depth defines the depth orientation The depth is defined from left to right deeper by default horizontal depth If Vertical Depth is selected the depth will mean from top to below deeper Canvas background color defines the background color of the visualization canvas Canvas grid enable disable and defines the background measurement grid parameters In Grid Type 5 types of grid are supported Basic Cross Horizontal Lines Vertical Lines Points and Cross Points Figure 3 10 User interface pref
57. n that you were working on But if the resources you loaded in your working session are all files in your local hard disk and you want to pass the working session to your colleague Please use the Export and Import functions under Core Archive menu in the File menu The Export function will pack all the resources along with a session cml file into a big compressed Core ARchive a car file It will contain all the images datasets annotations and their attachments within The other people can just use Import to open it up and restore everything you were working on his her screen 73 Chapter 10 Corelyzer server and plugin clients Corelyzer server and plugin support was developed by Arun Rao Yu Chung Julian Chen and Sangyoon James Lee in 2006 for supporting ANDRILL MIS Project 10 1 Server setup Before starting the server a few things must be prepared First the machine will need to have the Java Runtime Environment JRE 1 5 or greater Second a web server must be running Third configuration files will need to be made Setting up the JRE and a web server are beyond the scope of this document but many resources are available on the Web to do so The server program requires two files The first file contains the server settings and is specifically named server settings txt This file contains only four lines and are as follows the base web address for all annotation
58. nced software tools will allow geoscientists to integrate shipboard data entered into the JANUS database with 3rd party analyses of samples distributed to other scientists or generated by other programs and projects While doing this we will abstract the functional algorithms that drive NCLIP into software libraries that will be used in the CoreWall Suite so that they are available for other software development projects that want to build on these modules In this way the critical depth mapping functionality and enhancements that resulted in NCLIP will be integrated into the remarkable visualization capability that is CoreWall which is envisioned to be at the heart of a next generation suite of tools required by the IODP and other ocean science research programs as well as ICDP and other terrestrial core based research programs CoreWall s high resolution tiled LCD display gives geoscientists a large scale perspective helpful in processing and comparing high resolution digital line scan images of cores measuring up to hundreds of feet long A prototype desktop environment for CoreWall is Personal GeoWall2 PG2 a system that uses a single computer to drive four LCD panels as well as a single screen stereo GeoWall display CoreWall Affiliate Partners Oceanleadership Consortium USIO Science Services TAMU Integrated Ocean Drilling Program at Texas A amp M University CHRONOS ANDRILL Antarctic Geological Drilling Program LacCore U S Nation
59. nes in the header to describe the data file In the Data Range tab you can specify the actual data line range Notice that the first number in each in the lower File Content panel shows the line number starting from one In this example the actual data starts from 6th line till the very end of the file line 1586 In some equipments bad or invalid values will be recorded during data acquisition with some fixed numbers like 999 99 If you want to ignore these bad values check the Ignore some bad values checkbox and type in the designated value 49 Load and Plot Numerical Log Data Figure 6 3 Data range tab File Info Data Range Field Unir Label Depth Setup Fields Selection Start Rew and Ered Row End Line Number f 1 Ignore some bad value File Content 1 HOLE 7638 122 334 061005 574 851027 5 DEFTH SOR COR THOR URAN POTA amp 334 0610 2 7477 2 5013 0 3585 0278 0 0747 T 334 2134 2 7477 2 5013 0 3589 0278 0 0747 amp 134 3658 3 7477 2 5013 0 1585 O 0278 0747 9 494 5182 2 7477 2 5013 0 3589 0 0278 0 0747 10 334 6706 gr 5013 0 3583 0278 0 0747 L1 334 8230 2 7477 2 5013 0 3589 0 0278 0 0747 L 134 9754 ear 2 5019 0 3589 0278 0 0747 13 135 1278 3 7477 2 5013 0 1545 O 0278 Ora 14 335 2802 2 7477 2 5019 0 3589 0 0278 0 0747 15 335 4326 far 2 5013 0 1589 0 0276 0rd LG 335 5850 2 7477 2 5013 0 3588 0 0278 0 0747 1 335 7374 PATE 2 5013 0 3589 0278 0 0747 18 135 5858 3 7477 2 5013 0 3583 0
60. nfiguration you setup with your operating system See above sections The Display Configuration window will store your settings Once you have set this up the first time Corelyzer will load the saved configurations every time after without popping up the preferences window Rows Columns define how many monitors do you have and how they are arranged Screen Width Screen Height define the size of a single monitor in pixels If you start the Preferences configuration for the first time the full screen dimension will be used Screen DPI X Screen DPI Y DPI stands for dots per inch These defines the mapping from pixels to physical measurement In most cases you can leave them as default values Column Offset Row Offset Defines the offsets of the visualization area from the origin upper left corner of the primary monitor 20 Start Corelyzer Border Tickness The visualization takes into account the monitor border in tiled displays setup In most cases you can leave them with the default values Figure 3 9 Display Preferences Columns 1 925 Sormen Width Sereen Height 72 00 Screen DF X x Screen DPA Y Column Offset Bw Qiies Border Thickness enchees boc Top 34 Bonom jx Left 1 Righi Mee Came ee 3 2 3 User Interface Preferences Auto check version in startup if the program automatically check for latest update in startup Lock core section image if the program will make loaded sectio
61. on the section image the image will be highlighted by a yellow bounding box If you successfully do this the mouse pointer will change to a hand pointer The core section image will also be brought to the front of the other images This is noticeable if any of the core section images overlap At this point you can slide the section image left or right by moving your mouse left or right with Alt key pressed at the same time 7 1 4 Sliding a track A track can be slid vertically To do this first select a core section image and then hold down the Shift key The mouse pointer will remain looking like a hand cursor Move the mouse up or down and the track will be moved in the direction of the mouse motion NOTE Corelyzer loads all images and tracks at the origin It is recommended to slide a track away so that new images on a different track do not overlap an existing track 64 Interactions 7 2 Graph Plots 7 2 1 7 2 2 Graphs can be created after loading datasets that follow the Corelyzer Data XML Schema or plain text imports You can select to show it as line graph points or cross points Aside from creating a graph only track shown in the last chapter you can also create graphs by first right clicking on a section When you do this a pop up menu will appear Select the Graph option At this point the application will show a dialog window similar to Figure 7 10 If there is data for the selected section in a given data
62. ort Sheets Load an affine table Quit 320 Load a splice table Show IODF lists a 41 Load Images Affine table Splice tab Leg Site Hole Core Type Section Top 199 1217 A 1 H l 0 0L a99 FD OB a fo i 199 217 A l OHB 2g jox lio 217 pn HH Jox i 210 Aa p W p ow 199 217 A CH 9g Jo 1217 A 2 H 4 0 00 199 1217 A 2 H 5 0 00 199 1217 A 2 H 6 0 0C 199 1217 A 2 H Fi 0 00 199 1217 A 2 H 8 0 00 199 1217 A 3 H 1 0 00 199 1217 A 3 H 2 0 00 199 1217 A 3 H 3 0 00 199 1217 A 3 H 4 0 00 199 1217 A 3 H 5 0 0 199 1217 A 3 H 6 0 00 199 1217 A 3 H Fi 0 0L 199 1217 A 3 H B 0 0 199 1217 A 4 H 1 0 00 199 1217 A 4 H 2 0 00 199 1217 A 4 H 3 0 00 199 1217 A 4 H 4 0 00 199 1217 A 4 H 5 0 00 199 1217 A 4 H 6 0 00 1217 A 4 H Fi 0 00 Open Reset Load selected sections 42 Load Images 5 5 Load FMS images from IODP USIO logging database The Integrated Ocean Drilling Program United States Implementing Organization provides the logging database accessing service described in the webpage http brg ldeo columbia edu services The service serves not only numerical data but also some Formation MicroScanner FMS http www ldeo columbia edu BRG ODP LOGGING TOOLS fms html represented in image form stored in GIF format
63. oshop or The Gimp At this point we will assume that you are working with Photoshop In Photoshop you will want to view the image s properties by going to Image Image Size A dialog will appear showing the image width height etc If the resolution does not match the expected DPI then we will need to change it Before doing that make sure that the Resample Image checkbox is unchecked Otherwise when you change the DPI of the image the image will get resized After you uncheck the Resample Image option edit the Resolution text field and enter the correct DPI At the time of this writing most core section images have a DPI of 254 If you realize that more than one image contains the wrong DPI you can create a batch process in Photoshop to help you deal with all the images A 3 Corelyzer Data XML Schema The Corelyzer Data XML Schema is a fairly simple XML schema It is based off of a version of the Geotek data XML format Examples are available at Sample Data The root of the Corelyzer XML Schema is gt corewall_data lt Inside this node are blocks of section tags The XML schema is simply a set of tables one for each core section Inside section tags are tags to identify which section the table belongs to units of depth listing of fields and the data retrieved from sensors at particular depths Here is a complete example of the XML schema with sample data processed from JANUS 90 Appendix Figure A 1 Example native Co
64. pages the directory where the annotations are placed in the server for access the directory where the annotations are backed up to the last time that the server performed a backup lt backenabled or backupdisabled to enable or disable data backups Here is an example of that file http 131 193 77 222 corewallDB annotations Users corewallDB Sites annotations Users corewallDB Sites annotations 1155613264194 backupenabled NOTE The second last line should be 0 when first starting the server After which the server will automatically update that line every day The second file needed by the server is named users txt This file contains a listing of tuples that identifies a unique user The tuple is user name real name password The first three lines of the file describe the user name real name and password for the administrator of the server NOTE It should be stated that permissions to this file should be setup so that only the administrator has read and write permissions to the file An example of the file can be as follows admin 74 Corelyzer server and plugin clients 10 2 10 3 10 4 administrator admin arun Arun G Rao melodr matic jason Jason Leigh th3bo55 Anytime a new user is going to be created it is as easy as adding the user name real name and password to the end of the file Running the server To run the server you will need to perform the following
65. r eee eppure meruere teneri 7 2 2 Install Corelyz t 2 root pto pt ete E ep Pa eS aveo ee Eee e tapes 7 2 2 1 Microsoft Windows Users sessss eme ehe 7 2 2 2 Apple Mac OS X Users iet Ripe Pere remember aote bre 8 3 Start Corely Zetec lt 2 atre ec nei eee eenoas ley labs NRI DERRY TUER 10 3 1 Setting up the desktop environment 0 0 0 eee cece cece emere 10 3 1 1 Microsoft Windows Users esses em emm ee eere 10 3 1 2 Apple Mac OS X Users nce DRE e pner ra Rd Ere iesu E TS 16 3 2 Corelyzer Preferences i e epe ue peret per e epp PRAET PR IR SR RETE NUES 19 3 2 1 Directories Panel ie htt re RE Ere POR Eee td es e lenis 19 3 2 2 Display Preferences ecrit eerie derer eget es ete str erecto e EEE 20 3 2 3 User Interface Preferences ice Pre reet e EE ree OTROS 21 3 2 4 Session Sharing and DIS Preferences sssssseseee eece een eeneeeneeeneees 23 4 Corelyzer Layout iieri a rete ER pO Ete P Ee tt ebd etes ide re tenes 24 AV Tools Palette 2 tirer ree eph EU eaves ERES EUER 25 4 2 1Cores control windoW ined det tre ERR REN PSE STERNER Sse dun 25 42 T Menus uve IINE M REI p ERE IP eens RES 26 2 2 2 ocal Status eie eee vo e ere ete th atia vet C vo edem eius 26 4 2 3 Subscriptions asie oce tite ier ore sepe eri eene e pr der tg Ee 26 4 3 Visualization Canvas 4 iic reser tpe eee RE seas ee Pere ER er eee in EEE PESEE 27 5 Eoad mages nee energie pee
66. references ee seni i S t seria Dres te rye E EEEE ocv der Du ge Pe degens 21 3 10 User interface preferences 4 1 eene ph reed ss Ebr Pre PR Ee bero rie beet 22 4 1 Initial Corelyzer screen une eee eee uri Re ees iere pre pe LER 24 4 2 Tool Palette Functions 5 ert be tete rre eter RP E Patet eR er aboot dass 25 4 3 1Cores control window 5 eee ee eere p a rer perte etr epe dera aona 26 4 4 1Cores feed window 5 ie RID ee e re RE HEISE ONERA ES Ee 27 4 5 Visualization canvas with loaded core data sssssss e 28 5 1 Create a track i iioi cist canes ret sak nat e tre PEDE ETUR TE ae ee Ae e S E ve PR Te ERU NTN asa Peek 29 5 2 Load Images dialog a ceret tres tere rer ecg e pe rete qe roe sese be pg ce 30 5 3 Visualization canvas with loaded core section images sss 31 5 4 Online core image service query interface 1 0 0 0 eee cece cence eeceeeceeecaeeea seen esse eeu eees 32 5 5 Online core image service query oss ioo eter teret ere ads http aes ute E TERR niet 33 5 6 Adda new feed entsteht grec eR EEEN ESE 34 5 7 Specify feed URE inse ud DER ses RR HERR RH REP ERE 34 5 8 Refresh available lists 2 ttt eem etti e qe e EE E Ee E bee dett EEEE 35 3 9 Select to subscribe feeds oit trit e tere ERR pr PE pr RIDES 36 5 10 Select core image entries and right click 20 0 0 eee cence eece teen ceca cena sean eeaeeenneennees 38 5 11 Specify a track to hold selected core i
67. relyzer data XML file 1 arewall datas 2 xsect ions 3 lt ide12190_616h_63 id 4 lt depth_unitscm lt depth_units 5 lt field localid 1 namez HALC unitsz z B field localid 2 name HSIG unitzz Ti xdepthz3 678 depth 8 sensor idz B z88 15z sensor g sensor id 1 236 67 lt sensor gt 10 xdepthzs8 76B8 depth 11 sensor idz B z83 73 sensor 12 xlepthzl3 839 depth 13 sensor idz BH 83 b522 sensor 14 sensor idz 1 z37 21z sensor 15 sect ions 16 carewall data 91
68. right click E a File Edit Share Plugins Lists Tools Help B My Core Repository Core Listing Lecal Q Subscriptions SAFOD holeG a J TET Downloade SAFOD all Downloaded Leg 199 Site1215 Downloaded Download 5 Leg 199 5ite1216 N A image Remove Los 3144 10 CUT MX SO ines eee GeoRef Location Core Informationounnnary Hole E Run 1 Section 1 SE 00i Z UL te i i int a i a EEEEEEEEEE e Le 5 Select Load to download and load selected core images into Corelyzer Select or fill in the intented track name for these selected core images 38 Load Images Figure 5 11 Specify a track to hold selected core images Select a Track SAFOD hole G Click on OK will start the download and load process Click on the Local label at the left hand side to see if the selected sections are loaded 39 Load Images Figure 5 12 Images loaded with iCores feeds ew Rh 6 Sese Hide engin windaw Tals Lists File Share Hein Edit Plugins Suai Ir Session Track Sections Data Files Subrcrippnes TAFOD halit sS S025 1 E 1 2 SAFODD al 025 LE 0 3 Ling 199 Sen P15 Leg 199 5261216 Leg 199 See 1256 Hola E Run 1 Section 1 a a s E Has JEAN A screen capture video of these actions can be found in this link online size 10MB http www evl uic edu cavern corewall documents mo
69. rt applications fools use this order t determine the ma wersion of the Java Virtual Machine t use Restore Defaults Drag to change the preferred version Chapter 2 Download and Install Corelyzer 2 1 Download Corelyzer You can download copies of the application for the following platforms at the main download page http www evl uic edu cavern corewall downloads php http www w evl uic edu cavern corewall downloads php 2 2 Install Corelyzer 2 2 1 Microsoft Windows Users We provide an installer program for Windows users Please download the installer exe file from the download page http www evl uic edu cavern corewall downloads php double click the icon and follow the installer instructions Download and Install Corelyzer Figure 2 1 Corelyzer Windows Installer Fiy Locum anl pu x Welcome to the Corelyzer Setup Wizard Thr call iritall Corelrer on our compuner Rm receded tak ou close al cur appka Eelore torva ick Meat bocponiraae or Conci Ea edt Sebap sat Jagem 4 setup coretyzer 171 To return 16 pour Computer press Control X 2 2 2 Apple Mac OS X Users If you use Safari browser the application should be downloaded and extracted in your Downloads directory If you use other browsers please unzip the downloaded file double click it and you will get the application You can drag and drop the application in your preferred disk location like
70. rvice gesFilefcatalogMaere s EXP ZO fire 202 1259 B 1 H 3 0 000000 0 000000 t000000 Rater pomire lodp tara edu EOR rexteamy ak man re service sgesFileKcatalogNaene s EXP ZO Pheer 202 1218 B 1 H 4 0 000000 0 000000 4 500000 Atte pasm ce iodp tae educ EO R rerteavy ar man re serzice sgeth ilekcatalagNaene sEXP2O rec 20 12k8 B 1 H 5 0 009900 O0 0000900 amp 000000 Rates pme lodp tara educ OB rerteavy a amp man re weryice sgetFilefcatalogMaere s EXP TOP rec z02 12759 B 1 H CC 0 000000 0 000000 7 490000 htp ii pumice odp tam edu EOEO rextexvy ar man re ervicesgetldefcatalogNames XP 202 necordid s 8416 J 12k9 B 2 H 1 0 000900 0 000090 7 800000 Atte pusrmace lodp tara edu EOB reteary asman ne wervice egetlilelcatalogNaee S EXP Prec 202 LIFO B 2 H 2 0 000900 0 000000 9 100000 Kg pumice ind tara edu ORN reitit Aimi refwervice egetlilekzatalogNaeme EXPO there 203 LJEG B 2 H 3 0 000000 0 000000 10 800006 hing pamit odi tmu eda 2060 resheaky asman re Vereite s geil dete atalogName s XP 202 amp nerordids 4440 202 1250 B 2 H 4 0 000500 0 000000 17 300000 http pumin ted tama inda BOBO Jresbeacy icm rat iari gh des atalogNamss EXPT02 amp necordids d456 202 1239 B 2 H amp DORI 0 000000 13 800000 hoa pramscr nodo trm inda BOBO resDeaky asm niret derdcemqetF ame s EXPO Erererdids 4460 202 1230 B 2 H amp 0 000000 0 000050 15 300000 Mnp praece iaip tama eda BOBO re DRE rimam p dirici gh arme EXPZ02 amp recordid
71. s My Core Repository Main Pare Local Session Track Sections Data Files Fie Subscriptions Defaut Graph Track Mo fer SAFOD holeG Em co SAFOD all TTm8 Leg 199 Site1215 wl Leg 194 5ite 12 16 Leg 199 Site1256 Use mouse cursor to right click on the interested data file entry and click on the Graph menu item will bring up the Graph Dialog below 58 Load and Plot Numerical Log Data Figure 6 11 Graph dialog Choose a dataset 63B ngt xml i Apply to all sections in this dataset Choose graph section 763B ngt dat 0 763B ngt dat 1 763B ngt dat 2 7563B cotra 3 Properties fields Show Field Name H SGR THOR l POTA WING Value max 27 653 Scale max 27 653 Value min 2 683 Scale min 8 682 vi Collapse Graphs Apply Close You can select section by section and the available data fields will be shown in the Properties fields list below Check on the interested field checkboxes will plot the graph plot in the main visualization area registered to the depths 59 Load and Plot Numerical Log Data You can also check the Apply to all sections in this dataset to apply field selections to all sections in a dataset file When you select a field the field s maximum and minimum values will be updated below You can change the viewing maximum and minimum values to scale the graph plots You can also change the plot presentation and colors
72. s and click on the Load to load the log data into the plotting area OF COmelator ier e Lato e ctor etu ous Iit has gabe aen teo dette ce RU RD IEEE De ne eed etude Cases ds 84 11 5 Side by side Corelyzer and Correlator with log data plotted 1 0 0 0 eee cee eee ee eeee eee 85 11 6 Connect to Corelyzer button in Correlator command window eese 86 11 7 Confirmation of unload previously loaded images in Corelyzer eese 86 11 8 Creating 2 tie points in Correlator sosyetenin e aeneo mH mem enne 87 11 9 Adjusting tie points also updates core images sesss cece eeceeece tena cena eeu eeneeeenees 88 A l Example native Corelyzer data XML file ssssssssse Hee 91 Vil List of Tables 10 1 Commands reference table esssssssseseeseee e n me eme ee eme ee ese ee em esse ese serre 10 2 Handy scripts viii About CoreWall The CoreWall Suite is a collaborative development for a real time stratigraphic correlation core description CD and data visualization system to be used by the marine terrestrial and Antarctic science communities The development will be carried out in broad collaboration with stakeholders in these science communities To ensure that the software development does not occur independent of related IT activities in particular the development of the U S IODP Phase 2 Scientific Ocean Drilling Vessel SODV a Steering Committee will
73. s d470 202 1230 B2 H 7 0 000000 0 000000 T6 800000 h pumice ida nau eda BORO risbexky aiiman net servita m getFibele atalagM ame s EXP 202 amp nerordid 4445 202 1239 B 3 H l 0 0600 0 000000 17 300000 hp pa oda nam edu BOBO Jresbekgy as man pe deri ce m ge ieia 02 amp necor s Fi 1B H LI x 11 2 4 Load log data into Correlator plotting area Right click on the log data entries and select Load to load the data into the plotting area in the Correlator Figure 11 4 Right click on the data entries and click on the Load to load the log data into the plotting area of Correlator Data Enable Decimate Min Max updated Time by M T Root T 3 2 1234 Add new data A DENSITY MC RAN i 1 0 17 135 2009 01 18 21 18 julia B DEMSITY Enable an 1 D 16 Lay 2009 01 18 21 18 julia c DENSITY E Disable able 1 L2 135 2005 01 18 21 18 julian Downhole Log Data Delete Image Data Import cull table Table MAGE ae ble 3008 01 28 14 24 julia Saved Tables Stratigraphy 84 Fine tune with Correlator The data will be plotted in the Correlator window In the following screenshot it shows a 1920x1200 screen with Corelyzer showing in the left half and Correlator showing the right half with log data loaded and plotted Figure 11 5 Side by side Corelyzer and Correlator with log data plotted MIILILIAPuII E 11 2 5 Connect to Corelyzer from Correlator Click on the Connec
74. s preferences window you can specify your scratch disk location display settings and some user interface features Figure 3 7 Corelyzer Preferences Window A DD omn o ooo Diretorias Display k Corelyzer Preferences Initialization Welcome ew user Lani like you aec rinsing Corebyser For the First time Fici tale few minutes setting the preferences Bor Coryne Corchorr preferesees directory will be created in i corclyrer in your user home direciory Configuration files will be sved in there References Conall a Core Wall Wiki Cone Wall Bug Report amp Featurz Bogucs CHEE conn rp pof cim Heg m 3 2 1 Directories Panel Corelyzer will use part of your hard disk to store pre processed different levels of imagery blocks Also for some images that are not available in user s machine but their URLs are provided Corelyzer can download them to the download directory specified here It is recommended to select a bigger and fast hard disk 19 Start Corelyzer Figure 3 8 Directories preferences Ar Preference Dri Eri oto Dusgldane i a Image Block Directory Select Users i julian Documents Conehezer Cache Jimgblacks Dinard Danke Livy Seen Users f julian Documenti Corel rie Cached downloads C Help f Cancel o 3 2 2 Display Preferences Here you can set the display configuration that Corelyzer will use More often than not you will have it match the display co
75. t to Corelyzer button on the Correlator command window as shown in the following screenshot 85 Fine tune with Correlator Figure 11 6 Connect to Corelyzer button in Correlator command window Clear Ashis All Shifts SS All Splice Ties Clear All Ties A confirmation dialog will popup asking whether you want to unload previous loaded images in Corelyzer Click on YES will unload previous tracks and images in Corelyzer Figure 11 7 Confirmation of unload previously loaded images in Corelyzer Do you want to remove all loaded images 86 Fine tune with Correlator After successfully connected if the user use the scrollbar in Correlator to change the viewing depth range the view range will also be updated accordingly in the Corelyzer visualization area 11 2 6 Composite depth shifting with core images Core images will be loaded in the Corelyzer side if the connection between Correlator and Corelyzer is established during choosing both 2 tie points red and green points in Correlator A red horizontal line will appear in the Corelyzer as the reference tie depth Figure 11 8 Creating 2 tie points in Correlator corelyzer uisplashscreen SplashScreenMaln i Ww S m how Quit Carelymne FETTE Campanii made Hote Aor I epai 7 E Dragging the green tie point in Correlator like you always do it will update shift the core images accordingly like the data plots segments Yo
76. tation mode Help Once you are in creating annotation mode you can create a region of interest rectangle by pressing and dragging to show interested region A dialog asking for which kind of annotation you are creating will show up once you release the the mouse button Currently Corelyzer supports the following types of annotations Freefrom a threaded discussion freeform annotation Clast a structured annotation which keeps track of clastology information Sample Request a front end annotation for sample requests Property Values a generic property value pairs annotation Default properties is defined in the dictionary file specified in the preferences panel 67 Annotation Figure 8 3 Select annotation type i Pi Wherh kind of Annotatis Property Values Freeior Sample Request Edi i zc did Y EENEN og m No ud c ath Mun an en Tt 4 di jie 8 2 Reviewing and editing existing annotations After an annotation is created it can be edited in the future To edit an annotation or review it a user simply clicks on an annotation marker The same dialog used when creating an annotation will display Currently the comments will be attached into a discussion thread like display in a freeform annotation By clicking the tool buttons at the top of the editing area of annotation window the user can do simple HTML formatting and insert images and attachment files with URLs or by selecting files from loca
77. tched in the onscreen identify result and the display properties display as shown in the following two screenshots Figure 3 3 Example desktop configuration 14 Start Corelyzer Figure 3 4 Arrange desktops with drag and drop Lec The onion cars in maton Eee pho anangement ol pour Start Corelyzer 3 1 2 Apple Mac OS X Users To setup your monitors on your Mac you will need to get to the display settings To do this open the System Preferences application in your Applications directory Then choose Displays and you will see a dialog window on each monitor that is connected to your machine 16 Start Corelyzer Figure 3 5 Displays setup in System Preferences eoo System Preferences Gog Personal o sa D amp El o Appearance Dashboard amp Desktop amp Dock International Security Expos Screen Saver Hardware Bluetooth CDs amp DVDs Displays Energy Keyboard amp Print amp Fax Saver Mouse 5ound Internet amp Network e e Q Network QuickTime Sharing System u 2 9 Accounts Classic Date amp Time Software Update Other e mM i i ATI MenuMeters Norton Norton Displays Auto Protect QuickMenu Startup Disk 17 Start Corelyzer Make sure the display resolution on each monitor is the same After fixing the resolution go to your main window and select the Arrangement tab You will then see a layout of boxes that indicate how your monitors are laid out
78. the Applications directory or even your Desktop Double click the icon will launch the Corelyzer program Download and Install Corelyzer Figure 2 2 Corelyzer in Mac OS X Corelyzer 1 2 1 UB zip Corelyzer E Mac Xj Users julian E Desktop gj Corelyzer Install Chapter 3 Start Corelyzer 3 1 Setting up the desktop environment Before we start Corelyzer we must first make sure our display settings are correct On both the Mac and Windows the default monitor should be the upper left most monitor 3 1 1 Microsoft Windows Users To setup the monitors on windows you must first go to your Display You can do this by going to your Start menu selecting Control Panel and double clicking on Display 10 Start Corelyzer Figure 3 1 Display in Control Panel hi Aes Favorite Took ep Oua O 3 D Ome ET dress O conto Panel e sentio Conegery ves Accemwbd y paom Add Hardas Add re Mereen kimirin Pip imi Sae Asin A a 2 a Viren incite oa 1 Qi Fini and Support E Fors Game k hes i i ta m Per tnd Medus Dire Ones Pier engi Prieka Dac a 4 E k Deren ane Tsai diei T anie Security Center Toons Css del Er 4s e2 l S i ae wad Be kina drahy ECS Ej IET 9 oon 36 Ped LIS ENT cum 11 Start Corelyzer Once opened please go to the Settings tab Here you will see boxes with numbers and below those options that can b
79. then ask you to save the converted file in Corelyzer native xml format to your disk for future use After saving the data will be loaded into current Corelyzer session 54 Load and Plot Numerical Log Data Figure 6 7 Save converted file Save As 763B8 ngt xml I Desktop H Fh j i pM yzer 1 2 1 co E3 CRDownlcader data Friday January 9 2009 2908 PM E DiS Inerep Wednesday December 3 2008 5 18 PM T u D Phi pes aan aai SES B3 GenerareList ay February 2 2009 5 34 PM File Format XML file xml 4 New Folder Save D Notice that just like core images data plots have to belong to a track grouping So if you haven t have a track created or you want to have dedicated track grouping for data graph plots create a new track from the File menu 55 Load and Plot Numerical Log Data Figure 6 8 Create a track for data graph plot Please input the track name Graph Track tne GD A screen capture video of these actions can be found in this link online size 6 7MB http www evl uic edu cavern corewall documents movies 6 3 LoadCustomData mov 6 4 Download from IODP USIO logging database The Integrated Ocean Drilling Program United States Implementing Organization provides the logging database accessing service described in the webpage http brg ldeo columbia edu services To load logging data from the IODP USIO logging database select the IODP meun item from the
80. ts eve ee ee e ei vba ede ten end oR e b vel acd sd ere N edd 82 LDA AS tart CorelVZet c iecit ete eode eet Soa Coen ERE Deseret dens sen desee doeet eee 82 11 2 2 Start Correlator ceu Irc ERIS ERES S 82 11 2 3 Load log data tables and image list table A 82 11 2 4 Load log data into Correlator plotting area sseeR 84 11 2 5 Connect to Corelyzer from Correlator cece cece cece ceeeceeeee seca seca een eeneeens 85 11 2 6 Composite depth shifting with core images ss 87 12 Frequently Asked Questions FAQ neii a i eem ee hee ee hen nennen nnne nene 89 12 1 How do I compare two cores ssssssssssssesseee eee me eem enm enm emen men nenne 89 12 2 More question 2 dee et tette ne En et RE e oie Oron ette sot dese deeiqeh 89 A Appendbx 5 eret xn ndum Neu E 90 A 1 Why is the Image DPI Important ssessee HH eee 90 A 2 Making Sure the DPI of an Image is Correct ssssssssee e 90 A 3 Corelyzer Data XML Schema eet metet eire te iren 90 List of Figures 1 National Science Foundation Logo ssssnisiiosnors eiesinnige nisi Tae ehem men SE hene X 2 Electronic Visualization Laboratory Logo seseeeeseeeeeeeeenememe emen men mene rennen rennen X 3 LacCore Eog0 5i ose tret EINE EFE REPERI E REP eR Mi eR eERe X 4 Borehole Research Group LDEO Logo seeeee HH HH HII enr X 3 CoreWall LOZO E
81. u can use the core image texture for correlation reference 87 Fine tune with Correlator Figure 11 9 Adjusting tie points also updates core images Python F r View Window Help 2E oe hom A L TES BI IDEs nou GAL konge Quit Carelymne Composit merit If you right click the green tie point and select the Clear option the core images will be placed to their original position After your adjustments right click on the green tie point to choose adjustment option as described in Correlator document The core images will be positioned using the result affine table If you click on the Undo To button in the Correlator the affine table will be restored and re read by Corelyzer to shift core images according to the affine table When you disconnect from Corelyzer a dialog will popup in Corelyzer main window By default selecting YES it will close all opened core images during the composite session If you want to keep the arrangements setup on screen you can save the session file as described in the Save and Load Sessions 88 Chapter 12 Frequently Asked Questions FAQ 12 1 How do I compare two cores To compare 2 cores images or data side by side you can arrange cores to be compared in different tracks To do that first create and highlight a new track Then load first batch of images to be compared using Load images item in the File menu The second batch of core images can be
82. vies 5 3 LoadCoreCastImages mov 5 4 Load images using IODP formatted section list Click on the meun File gt IODP gt Load section list and select a section list file in format like example file attachments holeB dat remote image files and example file attachments A mac txt local image files will load and show the content of the list as shown in the following screen captures The section list file can be generated by any text editor or Excel You will have to save the file as tab separated format The file will need to include columns in order including Leg Site Hole Core 40 Load Images Type Section TopOffset BottomOffset Depth ImageLength and image file s source URL Currently the TopOffset and BottomOffset are not really used You can just fill in default value 0 0 Use mouse or keyboard to highlight the section that you want to load and click on the Load selected section button at the bottom will initial section images downloading and loading into Corelyzer Figure 5 13 Select load section list in IODP menu a Fe Edit Share Plugins Lists Tools He Create a Session N Create a Track AT Open Image Files 38M ain Panel Open Dataset Files 36D Session Track Sec Status Quick Data Import Custom Data Import Open a Session File 0 Recent Sessions Save db5 Save Session As A Core Archive t DIS IODP dM Load a section list Exp
83. your machine in order for the changes to take affect then do so Otherwise the resolution of your monitors will change and you will be prompted to keep the settings or change them back Note If your monitors do not support a particular resolution they will likely display that or they will stay black If you do not like your settings wait for some time and Windows will revert back After you have enabled your monitors and configured their display settings you should make sure that the layout of the monitors matches the layout of the boxes in your display settings First we need to identify which box represents which monitor and we can do this by seeing what number has been assigned to each monitor by Windows To do this click on the Identify button When you do this your monitors will display a number indicating which box refers to which monitor If your monitors are ordered differently than the boxes that are shown on your display settings then you will need to re arrange your monitors This is easily done by clicking and dragging the boxes in your settings window Again you should make sure that the upper left most box matches with your upper left most monitor and that monitor is enabled as your Primary Monitor Note that the desktop numbering in Microsoft Windows is depending on the order of how you connect monitors to graphic card connectors It may not appear in ascending order from left to right All you have to make sure is the ordering is ma

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